Merge branch 'main' into data-use-terms

kubernetes/loculus/templates/_common-metadata.tpl

@@ -28,12 +28,16 @@ fields:
     autocomplete: true
   - name: submittedAt
     type: timestamp
+    displayName: Date submitted
   - name: releasedAt
     type: timestamp
+    displayName: Date released
   - name: dataUseTerms
     type: string
     generateIndex: true
     autocomplete: true
+    displayName: Data use terms
+    initiallyVisible: true
     customDisplay:
       type: dataUseTerms
   - name: versionStatus
@@ -91,6 +95,9 @@ fields:
     {{- if .notSearchable }}
     notSearchable: {{ .notSearchable }}
     {{- end }}
+    {{- if .initiallyVisible }}
+    initiallyVisible: {{ .initiallyVisible }}
+    {{- end }}
     {{- if .displayName }}
     displayName: {{ .displayName }}
     {{- end }}

kubernetes/loculus/values.yaml

@@ -31,22 +31,28 @@ defaultOrganisms:
       metadata:
         - name: date
           type: date
+          initiallyVisible: true
         - name: region
           type: string
+          initiallyVisible: true
           generateIndex: true
           autocomplete: true
         - name: country
+          initiallyVisible: true
           type: string
           generateIndex: true
           autocomplete: true
         - name: division
+          initiallyVisible: true
           type: string
           generateIndex: true
           autocomplete: true
         - name: host
+          initiallyVisible: true
           type: string
           autocomplete: true
         - name: pango_lineage
+          initiallyVisible: true
           type: pango_lineage
           autocomplete: true
           required: true
@@ -273,6 +279,7 @@ defaultOrganisms:
           displayName: Collection date
           type: date
           required: true
+          initiallyVisible: true
         - name: ncbi_release_date
           displayName: NCBI release date
           type: date
@@ -281,6 +288,7 @@ defaultOrganisms:
           required: true
           generateIndex: true
           autocomplete: true
+          initiallyVisible: true
         - name: isolate_name
           displayName: Isolate name
           type: string

website/src/components/SearchPage/CustomizeModal.tsx

@@ -0,0 +1,97 @@
+import { Dialog, Transition } from '@headlessui/react';
+
+interface CheckboxFieldProps {
+    label: string;
+    checked: boolean;
+    onChange?: (event: React.ChangeEvent<HTMLInputElement>) => void;
+    disabled?: boolean;
+}
+
+const CheckboxField: React.FC<CheckboxFieldProps> = ({ label, checked, onChange, disabled }) => (
+    <div className='mb-2'>
+        <label className='flex items-center cursor-pointer'>
+            <input
+                type='checkbox'
+                checked={checked}
+                onChange={onChange}
+                className={`form-checkbox h-5 w-5 ${disabled !== true ? 'text-blue-600' : 'text-gray-300'}`}
+                disabled={disabled}
+            />
+            <span className='ml-2 text-gray-700'>{label}</span>
+        </label>
+    </div>
+);
+
+interface FieldValue {
+    name: string;
+    label: string;
+    isVisible?: boolean;
+    notSearchable?: boolean;
+}
+
+interface CustomizeModalProps {
+    isCustomizeModalOpen: boolean;
+    toggleCustomizeModal: () => void;
+    alwaysPresentFieldNames: string[];
+    fieldValues: FieldValue[];
+    handleFieldVisibilityChange: (fieldName: string, isVisible: boolean) => void;
+}
+
+export const CustomizeModal: React.FC<CustomizeModalProps> = ({
+    isCustomizeModalOpen,
+    toggleCustomizeModal,
+    alwaysPresentFieldNames,
+    fieldValues,
+    handleFieldVisibilityChange,
+}) => {
+    return (
+        <Transition appear show={isCustomizeModalOpen}>
+            <Dialog as='div' className='fixed inset-0 z-10 overflow-y-auto' onClose={toggleCustomizeModal}>
+                <div className='min-h-screen px-4 text-center'>
+                    <Dialog.Overlay className='fixed inset-0 bg-black opacity-30' />
+
+                    <span className='inline-block h-screen align-middle' aria-hidden='true'>
+                        &#8203;
+                    </span>
+
+                    <div className='inline-block w-full max-w-md p-6 my-8 overflow-hidden text-left align-middle transition-all transform bg-white shadow-xl rounded-2xl text-sm'>
+                        <Dialog.Title as='h3' className='text-lg font-medium leading-6 text-gray-900'>
+                            Customize Search Fields
+                        </Dialog.Title>
+
+                        <div className='mt-4 text-gray-700 text-sm'>Toggle the visibility of search fields</div>
+
+                        <div className='mt-4'>
+                            {alwaysPresentFieldNames.map((fieldName) => (
+                                <CheckboxField key={fieldName} label={fieldName} checked disabled />
+                            ))}
+
+                            {fieldValues
+                                .filter((field) => field.notSearchable !== true)
+                                .map((field) => (
+                                    <CheckboxField
+                                        key={field.name}
+                                        label={field.label}
+                                        checked={field.isVisible !== false}
+                                        onChange={(e) => {
+                                            handleFieldVisibilityChange(field.name, e.target.checked);
+                                        }}
+                                    />
+                                ))}
+                        </div>
+
+                        <div className='mt-6'>
+                            <button
+                                type='button'
+                                className='inline-flex justify-center px-4 py-2 text-sm font-medium text-blue-900 bg-blue-100 border border-transparent rounded-md hover:bg-blue-200 focus:outline-none focus-visible:ring-2 focus-visible:ring-offset-2 focus-visible:ring-blue-500'
+                                onClick={toggleCustomizeModal}
+                            >
+                                Close
+                            </button>
+                        </div>
+                    </div>
+                </div>
+            </Dialog>
+        </Transition>
+    );
+};

website/src/components/SearchPage/SearchForm.spec.tsx

@@ -10,6 +10,16 @@ import type { MetadataFilter } from '../../types/config.ts';
 import type { ReferenceGenomesSequenceNames } from '../../types/referencesGenomes.ts';
 import type { ClientConfig } from '../../types/runtimeConfig.ts';
 
+global.ResizeObserver = class FakeResizeObserver {
+    // This is needed or we get a test failure: https://github.com/tailwindlabs/headlessui/discussions/2414
+    // eslint-disable-next-line @typescript-eslint/explicit-member-accessibility, @typescript-eslint/no-empty-function
+    observe() {}
+    // eslint-disable-next-line @typescript-eslint/explicit-member-accessibility, @typescript-eslint/no-empty-function
+    disconnect() {}
+    // eslint-disable-next-line @typescript-eslint/explicit-member-accessibility, @typescript-eslint/no-empty-function
+    unobserve() {}
+};
+
 const searchButtonText = 'Search sequences';
 
 vi.mock('../../config', () => ({
@@ -20,9 +30,30 @@ vi.mock('../../config', () => ({
 const queryClient = new QueryClient();
 
 const defaultSearchFormFilters = [
-    { name: 'field1', type: 'string' as const, label: 'Field 1', autocomplete: false, filterValue: '' },
-    { name: 'field2', type: 'date' as const, autocomplete: false, filterValue: '', label: 'Field 2' },
-    { name: 'field3', type: 'pango_lineage' as const, label: 'Field 3', autocomplete: true, filterValue: '' },
+    {
+        name: 'field1',
+        type: 'string' as const,
+        label: 'Field 1',
+        autocomplete: false,
+        filterValue: '',
+        initiallyVisible: true,
+    },
+    {
+        name: 'field2',
+        type: 'date' as const,
+        autocomplete: false,
+        filterValue: '',
+        label: 'Field 2',
+        initiallyVisible: true,
+    },
+    {
+        name: 'field3',
+        type: 'pango_lineage' as const,
+        label: 'Field 3',
+        autocomplete: true,
+        filterValue: '',
+        initiallyVisible: true,
+    },
 ];
 
 const defaultReferenceGenomesSequenceNames = {
@@ -90,6 +121,7 @@ describe('SearchForm', () => {
                 autocomplete: false,
                 filterValue: '',
                 notSearchable: true,
+                initiallyVisible: true,
             },
         ]);
 
@@ -104,6 +136,7 @@ describe('SearchForm', () => {
                 name: timestampFieldName,
                 type: 'timestamp' as const,
                 filterValue: '1706147200',
+                initiallyVisible: true,
             },
         ]);
 
@@ -128,6 +161,7 @@ describe('SearchForm', () => {
                 name: dateFieldName,
                 type: 'date' as const,
                 filterValue: '2024-01-25',
+                initiallyVisible: true,
             },
         ]);
         const dateLabel = screen.getByText('Date field');
@@ -143,4 +177,23 @@ describe('SearchForm', () => {
 
         expect(window.location.href).toContain(`${dateFieldName}=2025-01-25`);
     });
+
+    test('toggle field visibility', async () => {
+        renderSearchForm();
+
+        expect(screen.getByLabelText('Field 1')).toBeVisible();
+
+        const customizeButton = screen.getByRole('button', { name: 'Customize fields' });
+        await userEvent.click(customizeButton);
+
+        const field1Checkbox = screen.getByRole('checkbox', { name: 'Field 1' });
+        expect(field1Checkbox).toBeChecked();
+
+        await userEvent.click(field1Checkbox);
+
+        const closeButton = screen.getByRole('button', { name: 'Close' });
+        await userEvent.click(closeButton);
+
+        expect(screen.queryByLabelText('Field 1')).not.toBeInTheDocument();
+    });
 });

website/src/components/SearchPage/SearchForm.tsx

@@ -3,6 +3,7 @@ import { QueryClient, QueryClientProvider } from '@tanstack/react-query';
 import { sentenceCase } from 'change-case';
 import { type FC, type FormEventHandler, useMemo, useState, useCallback } from 'react';
 
+import { CustomizeModal } from './CustomizeModal.tsx';
 import { AccessionField } from './fields/AccessionField.tsx';
 import { AutoCompleteField, type AutoCompleteFieldProps } from './fields/AutoCompleteField';
 import { DateField, TimestampField } from './fields/DateField.tsx';
@@ -50,12 +51,16 @@ export const SearchForm: FC<SearchFormProps> = ({
         fieldList.map((filter) => ({
             ...filter,
             label: filter.label ?? filter.displayName ?? sentenceCase(filter.name),
+            isVisible: filter.initiallyVisible ?? false,
         })),
     );
+
+    const alwaysPresentFieldNames = ['Accession', 'Mutation'];
     const [accessionFilter, setAccessionFilter] = useState<AccessionFilter>(initialAccessionFilter);
     const [mutationFilter, setMutationFilter] = useState<MutationFilter>(initialMutationFilter);
     const [isLoading, setIsLoading] = useState(false);
     const { isOpen: isMobileOpen, close: closeOnMobile, toggle: toggleMobileOpen } = useOffCanvas();
+    const [isCustomizeModalOpen, setIsCustomizeModalOpen] = useState(false);
 
     const handleFieldChange = useCallback(
         (metadataName: string, filter: string) => {
@@ -112,10 +117,15 @@ export const SearchForm: FC<SearchFormProps> = ({
     const fields = useMemo(
         () =>
             fieldValues.map((field) => {
+                if (field.isVisible !== true) {
+                    return null;
+                }
                 if (field.grouped === true) {
                     return (
                         <div key={field.name} className='flex flex-col border p-3 mb-3 rounded-md border-gray-300'>
-                            <h3 className='text-gray-500 text-sm mb-1'>{field.label}</h3>
+                            <h3 className='text-gray-500 text-sm mb-1'>
+                                {field.displayName !== undefined ? field.displayName : field.label}
+                            </h3>
 
                             {field.groupedFields.map((groupedField) => (
                                 <SearchField
@@ -145,6 +155,38 @@ export const SearchForm: FC<SearchFormProps> = ({
         [fieldValues, handleFieldChange, isLoading, lapisUrl, flattenedFieldValues],
     );
 
+    const toggleCustomizeModal = () => {
+        setIsCustomizeModalOpen(!isCustomizeModalOpen);
+    };
+
+    const clearValues = (possiblyGroupedFieldName: string) => {
+        const fieldInQuestion = fieldValues.find((field) => field.name === possiblyGroupedFieldName);
+        if (fieldInQuestion === undefined) {
+            return;
+        }
+
+        if (fieldInQuestion.grouped === true) {
+            for (const groupedField of fieldInQuestion.groupedFields) {
+                handleFieldChange(groupedField.name, '');
+            }
+        } else {
+            handleFieldChange(possiblyGroupedFieldName, '');
+        }
+    };
+    const handleFieldVisibilityChange = (fieldName: string, isVisible: boolean) => {
+        if (isVisible === false) {
+            clearValues(fieldName);
+        }
+        setFieldValues((prev) =>
+            prev.map((field) => {
+                if (field.name === fieldName) {
+                    return { ...field, isVisible };
+                }
+                return field;
+            }),
+        );
+    };
+
     return (
         <QueryClientProvider client={queryClient}>
             <div className='text-right -mb-10 md:hidden'>
@@ -162,13 +204,20 @@ export const SearchForm: FC<SearchFormProps> = ({
                 <div className='shadow-xl rounded-r-lg px-4 pt-4'>
                     <div className='flex'>
                         <h2 className='text-lg font-semibold flex-1 md:hidden'>Search query</h2>
-                        <button className='underline' onClick={resetSearch}>
-                            Reset
-                        </button>
+                        <div className='flex items-center justify-between w-full mb-2 text-primary-700'>
+                            <button className='underline' onClick={toggleCustomizeModal}>
+                                Customize fields
+                            </button>
+
+                            <button className='underline' onClick={resetSearch}>
+                                Reset
+                            </button>
+                        </div>
                         <button className='ml-4 md:hidden' onClick={closeOnMobile}>
                             <SandwichIcon isOpen />
                         </button>
                     </div>
+
                     <form onSubmit={handleSearch}>
                         <div className='flex flex-col'>
                             <AccessionField initialValue={initialAccessionFilter} onChange={setAccessionFilter} />
@@ -191,6 +240,13 @@ export const SearchForm: FC<SearchFormProps> = ({
                     </form>
                 </div>
             </div>
+            <CustomizeModal
+                isCustomizeModalOpen={isCustomizeModalOpen}
+                toggleCustomizeModal={toggleCustomizeModal}
+                alwaysPresentFieldNames={alwaysPresentFieldNames}
+                fieldValues={fieldValues}
+                handleFieldVisibilityChange={handleFieldVisibilityChange}
+            />
         </QueryClientProvider>
     );
 };
@@ -267,6 +323,9 @@ const consolidateGroupedFields = (filters: MetadataFilter[]): (MetadataFilter |
                     groupedFields: [],
                     type: filter.type,
                     grouped: true,
+                    displayName: filter.fieldGroupDisplayName,
+                    label: filter.label,
+                    initiallyVisible: filter.initiallyVisible,
                 };
                 fieldList.push(fieldForGroup);
                 groupsMap.set(filter.fieldGroup, fieldForGroup);