@genspectrum/dashboard-components 0.9.1 → 0.10.0

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@genspectrum/dashboard-components",
-    "version": "0.9.1",
+    "version": "0.10.0",
     "description": "GenSpectrum web components for building dashboards",
     "type": "module",
     "license": "AGPL-3.0-only",

package/src/preact/components/confidence-interval-selector.tsx

@@ -20,7 +20,7 @@ export const ConfidenceIntervalSelector: FunctionComponent<ConfidenceIntervalSel
 
     const items = [
         { label: 'Confidence interval method', value: 'none', disabled: true },
-        ...confidenceIntervalMethods.concat('none').map((method) => {
+        ...confidenceIntervalMethods.map((method) => {
             switch (method) {
                 case 'wilson':
                     return { label: 'Wilson, 95% CI', value: 'wilson' };

package/src/preact/mutationFilter/parseMutation.spec.ts

@@ -35,6 +35,16 @@ describe('parseMutation', () => {
                 input: 'ins_gene1:10:ACGT',
                 expected: { type: 'aminoAcidInsertions', value: new InsertionClass('gene1', 10, 'ACGT') },
             },
+            {
+                name: 'should parse amino acid insertions in all upper case',
+                input: 'INS_GENE1:10:ACGT',
+                expected: { type: 'aminoAcidInsertions', value: new InsertionClass('GENE1', 10, 'ACGT') },
+            },
+            {
+                name: 'should parse amino acid insertions in all lower case',
+                input: 'ins_gene1:10:acgt',
+                expected: { type: 'aminoAcidInsertions', value: new InsertionClass('gene1', 10, 'acgt') },
+            },
             {
                 name: 'should parse amino acid insertion with LAPIS-style wildcard',
                 input: 'ins_gene1:10:?AC?GT',
@@ -78,6 +88,16 @@ describe('parseMutation', () => {
                 input: 'gene1:A123-',
                 expected: { type: 'aminoAcidMutations', value: new DeletionClass('gene1', 'A', 123) },
             },
+            {
+                name: 'should parse amino acid deletion in all upper case',
+                input: 'GENE1:A123-',
+                expected: { type: 'aminoAcidMutations', value: new DeletionClass('GENE1', 'A', 123) },
+            },
+            {
+                name: 'should parse amino acid deletion in all lower case',
+                input: 'gene1:a123-',
+                expected: { type: 'aminoAcidMutations', value: new DeletionClass('gene1', 'a', 123) },
+            },
             {
                 name: 'should parse amino acid deletion without valueAtReference',
                 input: 'gene1:123-',
@@ -123,6 +143,16 @@ describe('parseMutation', () => {
                 input: 'gene1:A123T',
                 expected: { type: 'aminoAcidMutations', value: new SubstitutionClass('gene1', 'A', 'T', 123) },
             },
+            {
+                name: 'should parse amino acid substitution in all upper case',
+                input: 'GENE1:A123T',
+                expected: { type: 'aminoAcidMutations', value: new SubstitutionClass('GENE1', 'A', 'T', 123) },
+            },
+            {
+                name: 'should parse amino acid substitution in all lower case',
+                input: 'gene1:a123t',
+                expected: { type: 'aminoAcidMutations', value: new SubstitutionClass('gene1', 'a', 't', 123) },
+            },
             {
                 name: 'should return null for substitution with segment not in reference genome',
                 input: 'notInReferenceGenome:A123T',

package/src/preact/mutationFilter/sequenceTypeFromSegment.ts

@@ -9,11 +9,12 @@ export const sequenceTypeFromSegment = (
         return isSingleSegmented(referenceGenome) ? 'nucleotide' : undefined;
     }
 
-    if (referenceGenome.nucleotideSequences.some((sequence) => sequence.name === possibleSegment)) {
+    const segment = possibleSegment.toLowerCase();
+    if (referenceGenome.nucleotideSequences.some((sequence) => sequence.name.toLowerCase() === segment)) {
         return 'nucleotide';
     }
 
-    if (referenceGenome.genes.some((gene) => gene.name === possibleSegment)) {
+    if (referenceGenome.genes.some((gene) => gene.name.toLowerCase() === segment)) {
         return 'amino acid';
     }
     return undefined;

package/src/preact/prevalenceOverTime/prevalence-over-time.stories.tsx

@@ -30,7 +30,7 @@ export default {
             control: { type: 'check' },
         },
         confidenceIntervalMethods: {
-            options: ['wilson'],
+            options: ['none', 'wilson'],
             control: { type: 'check' },
         },
         width: { control: 'text' },
@@ -73,7 +73,7 @@ export const TwoVariants: StoryObj<PrevalenceOverTimeProps> = {
         granularity: 'month',
         smoothingWindow: 0,
         views: ['bar', 'line', 'bubble', 'table'],
-        confidenceIntervalMethods: ['wilson'],
+        confidenceIntervalMethods: ['none', 'wilson'],
         width: '100%',
         height: '700px',
         lapisDateField: 'date',
@@ -147,7 +147,7 @@ export const OneVariant: StoryObj<PrevalenceOverTimeProps> = {
         granularity: 'day',
         smoothingWindow: 7,
         views: ['bar', 'line', 'bubble', 'table'],
-        confidenceIntervalMethods: ['wilson'],
+        confidenceIntervalMethods: ['none', 'wilson'],
         width: '100%',
         height: '700px',
         lapisDateField: 'date',
@@ -205,7 +205,7 @@ export const ShowsNoDataBanner: StoryObj<PrevalenceOverTimeProps> = {
         granularity: 'day',
         smoothingWindow: 7,
         views: ['bar', 'line', 'bubble', 'table'],
-        confidenceIntervalMethods: ['wilson'],
+        confidenceIntervalMethods: ['none', 'wilson'],
         width: '100%',
         height: '700px',
         lapisDateField: 'date',

package/src/preact/prevalenceOverTime/prevalence-over-time.tsx

@@ -1,5 +1,5 @@
 import { type FunctionComponent } from 'preact';
-import { useContext, useState } from 'preact/hooks';
+import { useContext, useEffect, useState } from 'preact/hooks';
 
 import { getPrevalenceOverTimeTableData } from './getPrevalenceOverTimeTableData';
 import PrevalenceOverTimeBarChart from './prevalence-over-time-bar-chart';
@@ -97,6 +97,16 @@ const PrevalenceOverTimeTabs: FunctionComponent<PrevalenceOverTimeTabsProps> = (
     const [confidenceIntervalMethod, setConfidenceIntervalMethod] = useState<ConfidenceIntervalMethod>(
         confidenceIntervalMethods.length > 0 ? confidenceIntervalMethods[0] : 'none',
     );
+
+    useEffect(() => {
+        setConfidenceIntervalMethod((confidenceIntervalMethod) => {
+            if (!confidenceIntervalMethods.includes(confidenceIntervalMethod)) {
+                return confidenceIntervalMethods.length > 0 ? confidenceIntervalMethods[0] : 'none';
+            }
+            return confidenceIntervalMethod;
+        });
+    }, [confidenceIntervalMethods]);
+
     const yAxisMaxConfig = { linear: yAxisMaxLinear, logarithmic: yAxisMaxLogarithmic };
 
     const getTab = (view: View) => {

package/src/utils/mutations.ts

@@ -14,7 +14,7 @@ export interface MutationClass extends Mutation {
 }
 
 export const substitutionRegex =
-    /^((?<segment>[A-Za-z0-9_-]+)(?=:):)?(?<valueAtReference>[A-Za-z])?(?<position>\d+)(?<substitutionValue>[A-Za-z.])?$/;
+    /^((?<segment>[A-Z0-9_-]+)(?=:):)?(?<valueAtReference>[A-Z])?(?<position>\d+)(?<substitutionValue>[A-Z.])?$/i;
 
 export interface Substitution extends Mutation {
     type: 'substitution';
@@ -68,7 +68,7 @@ export class SubstitutionClass implements MutationClass, Substitution {
     }
 }
 
-export const deletionRegex = /^((?<segment>[A-Za-z0-9_-]+)(?=:):)?(?<valueAtReference>[A-Za-z])?(?<position>\d+)(-)$/;
+export const deletionRegex = /^((?<segment>[A-Z0-9_-]+)(?=:):)?(?<valueAtReference>[A-Z])?(?<position>\d+)(-)$/i;
 
 export interface Deletion extends Mutation {
     type: 'deletion';
@@ -119,7 +119,7 @@ export class DeletionClass implements MutationClass, Deletion {
 }
 
 export const insertionRegexp =
-    /^ins_((?<segment>[A-Za-z0-9_-]+)(?=:):)?(?<position>\d+):(?<insertedSymbols>(([A-Za-z?]|(\.\*))+))$/i;
+    /^ins_((?<segment>[A-Z0-9_-]+)(?=:):)?(?<position>\d+):(?<insertedSymbols>(([A-Z?]|(\.\*))+))$/i;
 
 export interface Insertion extends Mutation {
     type: 'insertion';

package/src/web-components/visualization/gs-prevalence-over-time.stories.ts

@@ -46,7 +46,7 @@ const meta: Meta<Required<PrevalenceOverTimeProps>> = {
             control: { type: 'check' },
         },
         confidenceIntervalMethods: {
-            options: ['wilson'],
+            options: ['none', 'wilson'],
             control: { type: 'check' },
         },
         width: { control: 'text' },

package/src/web-components/visualization/gs-prevalence-over-time.tsx

@@ -103,11 +103,11 @@ export class PrevalenceOverTimeComponent extends PreactLitAdapterWithGridJsStyle
 
     /**
      * A list of methods to calculate the confidence interval.
-     * The option `none` is always available and disables confidence intervals.
      * Pass an empty array to disable the confidence interval selector.
+     * The first entry will be selected by default.
      */
     @property({ type: Array })
-    confidenceIntervalMethods: ('wilson' | 'none')[] = ['wilson'];
+    confidenceIntervalMethods: ('wilson' | 'none')[] = ['none', 'wilson'];
 
     /**
      * The width of the component.