Docs work in progress

website/docs/components.md

@@ -0,0 +1,315 @@
+# Components
+
+## React components
+
+* `src/components/ErrorReportInstruction.tsx`
+
+    - ErrorReportToastModal
+    - ErrorReportInstruction
+    - CopyToClipboardButton
+
+* `src/components/auth/LoginButton.tsx`
+
+    - LoginButton: `<button>`
+
+* `src/components/genspectrum/AdvancedQueryFilter.tsx`
+
+    - AdvancedQueryFilter({value?: string, onInput?: ChangeEventHandler<HTMLInputElement>}): `<input  placeholder={'Advanced query: A123T & ins_123:TA'}` -- how is this hooked up? via the onInput, but not type restricted.
+
+* `src/components/genspectrum/GsApp.tsx`
+
+    - GsApp: just `<gs-app>`
+
+* `src/components/genspectrum/GsDateRangeSelector.tsx`
+
+    - GsDateRangeSelector: `<gs-date-range-selector>` with useEffect
+
+* `src/components/genspectrum/GsLineageFilter.tsx`
+
+    - GsLineageFilter: `<gs-lineage-filter` with useEffect
+
+* `src/components/genspectrum/GsLocationFilter.tsx`
+
+    - GsLocationFilter: `<gs-location-filter` with useEffect
+
+* `src/components/genspectrum/GsMutationFilter.tsx`
+
+    - GsMutationFilter: `<gs-mutation-filter` with useEffect
+
+* `src/components/genspectrum/GsNumberSequencesOverTime.tsx`
+
+    - `GsNumberSequencesOverTime: `<gs-number-sequences-over-time`
+
+* `src/components/genspectrum/GsPrevalenceOverTime.tsx`
+
+    - `GsPrevalenceOverTime`: `<gs-prevalence-over-time`
+
+* `src/components/genspectrum/GsTextInput.tsx`
+
+    - `GsTextInput`: `<gs-text-input` with useEffect
+
+* `src/components/pageStateSelectors/ApplyFilterButton.tsx`
+
+    - `ApplyFilterButton`: `<a role='button'`
+
+* `src/components/pageStateSelectors/BaselineSelector.tsx`
+
+    - `BaselineSelector`: `<div className='flex flex-col gap-2'> <GsLocationFilter .. <GsDateRangeSelector`
+
+* `src/components/pageStateSelectors/CompareSideBySidePageStateSelector.tsx`
+* `src/components/pageStateSelectors/CompareVariantsPageStateSelector.tsx`
+* `src/components/pageStateSelectors/CompareVariantsToBaselineStateSelector.tsx`
+* `src/components/pageStateSelectors/FallbackElement.tsx`
+* `src/components/pageStateSelectors/LineageFilterInput.tsx`
+* `src/components/pageStateSelectors/SelectorHeadline.tsx`
+* `src/components/pageStateSelectors/SequencingEffortsPageStateSelector.tsx`
+* `src/components/pageStateSelectors/SingleVariantPageStateSelector.tsx`
+* `src/components/pageStateSelectors/VariantSelector.tsx`
+* `src/components/pageStateSelectors/VariantsSelector.tsx`
+* `src/components/subscriptions/backendApi/withQueryProvider.tsx`
+* `src/components/subscriptions/create/BaselineInput.tsx`
+* `src/components/subscriptions/create/ChannelsInput.tsx`
+* `src/components/subscriptions/create/CountFilterInput.tsx`
+* `src/components/subscriptions/create/DateWindowInput.tsx`
+* `src/components/subscriptions/create/FilterDisplay.tsx`
+* `src/components/subscriptions/create/IntervalInput.tsx`
+* `src/components/subscriptions/create/NameInput.tsx`
+* `src/components/subscriptions/create/OrganismInput.tsx`
+* `src/components/subscriptions/create/SubscriptionsCreate.tsx`
+* `src/components/subscriptions/create/TriggerInput.tsx`
+* `src/components/subscriptions/create/TriggerTypeInput.tsx`
+* `src/components/subscriptions/create/VariantInput.tsx`
+* `src/components/subscriptions/notificationChannels/NotificationChannelDisplay.tsx`
+* `src/components/subscriptions/overview/SubscriptionDisplay.tsx`
+* `src/components/subscriptions/overview/SubscriptionEntry.tsx`
+* `src/components/subscriptions/overview/SubscriptionFilter.tsx`
+* `src/components/subscriptions/overview/Subscriptions.tsx`
+* `src/components/views/analyzeSingleVariant/CollectionsList.tsx`
+* `src/layouts/Breadcrumbs.tsx`
+* `src/layouts/base/header/Brand.tsx`
+* `src/layouts/base/header/MegaMenu.tsx`
+* `src/layouts/base/header/Navigation.tsx`
+* `src/styles/containers/BorderedCard.tsx`
+* `src/styles/containers/CardContent.tsx`
+* `src/styles/containers/CardDescription.tsx`
+* `src/styles/containers/CardHeader.tsx`
+* `src/styles/containers/DividerList.tsx`
+* `src/styles/containers/Modal.tsx`
+* `src/styles/containers/ModalBox.tsx`
+* `src/styles/containers/ModalContent.tsx`
+* `src/styles/containers/ModalHeader.tsx`
+* `src/styles/containers/PageContainer.tsx`
+* `src/styles/containers/PageHeadline.tsx`
+* `src/styles/input/InputLabel.tsx`
+
+## Astro components
+
+* `src/components/ComponentHeadline.astro`
+* `src/components/ComponentWrapper.astro`
+* `src/components/ComponentsGrid.astro`
+* `src/components/InfluenzaWastewaterInfo.astro`
+* `src/components/Link.astro`
+* `src/components/MainMenuItem.astro`
+* `src/components/RsvWastewaterInfo.astro`
+* `src/components/auth/LoginState.astro`
+* `src/components/auth/NotLoggedIn.astro`
+* `src/components/auth/UserDropdown.astro`
+* `src/components/genspectrum/GsAggregate.astro`
+* `src/components/genspectrum/GsMutationComparison.astro`
+* `src/components/genspectrum/GsMutations.astro`
+* `src/components/genspectrum/GsMutationsOverTime.astro`
+* `src/components/genspectrum/GsNumberSequencesOverTime.astro`
+* `src/components/genspectrum/GsPrevalenceOverTime.astro`
+* `src/components/genspectrum/GsRelativeGrowthAdvantage.astro`
+* `src/components/genspectrum/GsSequencesByLocation.astro`
+* `src/components/genspectrum/GsStatistics.astro`
+* `src/components/genspectrum/GsWastewaterMutationsOverTime.astro`
+* `src/components/views/analyzeSingleVariant/GenericAnalyzeSingleVariantPage.astro`
+* `src/components/views/analyzeSingleVariant/SelectVariant.astro`
+* `src/components/views/compareSideBySide/GenericCompareSideBySidePage.astro`
+* `src/components/views/compareToBaseline/GenericCompareToBaselinePage.astro`
+* `src/components/views/compareToBaseline/SelectBaseline.astro`
+* `src/components/views/compareVariants/GenericCompareVariantsPage.astro`
+* `src/components/views/compareVariants/SelectVariants.astro`
+* `src/components/views/sequencingEfforts/GenericSequencingEffortsPage.astro`
+* `src/layouts/ContaineredPage/ContaineredPageLayout.astro`
+* `src/layouts/OrganismPage/AccessionsDownloadButton.astro`
+* `src/layouts/OrganismPage/DataPageLayout.astro`
+* `src/layouts/OrganismPage/LastUpdatedInfo.astro`
+* `src/layouts/OrganismPage/OrganismViewPageLayout.astro`
+* `src/layouts/OrganismPage/SingleVariantOrganismPageLayout.astro`
+* `src/layouts/base/BaseLayout.astro`
+* `src/layouts/base/footer/DataInfo.astro`
+* `src/layouts/base/footer/DataOriginLink.astro`
+* `src/layouts/base/footer/Footer.astro`
+* `src/layouts/base/footer/FooterNavigation.astro`
+* `src/layouts/base/footer/PrimaryFooter.astro`
+* `src/layouts/base/footer/SecondaryFooter.astro`
+* `src/layouts/base/header/CallToAction.astro`
+* `src/layouts/base/header/HamburgerMenu.astro`
+* `src/layouts/base/header/HamburgerMenuItem.astro`
+* `src/layouts/base/header/HamburgerMenuSection.astro`
+* `src/layouts/base/header/Header.astro`
+* `src/pages/404.astro`
+* `src/pages/500.astro`
+* `src/pages/covid/compare-side-by-side.astro`
+* `src/pages/covid/compare-to-baseline.astro`
+* `src/pages/covid/compare-variants.astro`
+* `src/pages/covid/index.astro`
+* `src/pages/covid/sequencing-efforts.astro`
+* `src/pages/covid/single-variant.astro`
+* `src/pages/data.astro`
+* `src/pages/flu/compare-side-by-side.astro`
+* `src/pages/flu/h5n1/compare-side-by-side.astro`
+* `src/pages/flu/h5n1/compare-to-baseline.astro`
+* `src/pages/flu/h5n1/compare-variants.astro`
+* `src/pages/flu/h5n1/index.astro`
+* `src/pages/flu/h5n1/sequencing-efforts.astro`
+* `src/pages/flu/h5n1/single-variant.astro`
+* `src/pages/flu/index.astro`
+* `src/pages/flu/sequencing-efforts.astro`
+* `src/pages/index.astro`
+* `src/pages/logout.astro`
+* `src/pages/mpox/compare-side-by-side.astro`
+* `src/pages/mpox/compare-to-baseline.astro`
+* `src/pages/mpox/compare-variants.astro`
+* `src/pages/mpox/index.astro`
+* `src/pages/mpox/sequencing-efforts.astro`
+* `src/pages/mpox/single-variant.astro`
+* `src/pages/rsv-a/compare-side-by-side.astro`
+* `src/pages/rsv-a/compare-to-baseline.astro`
+* `src/pages/rsv-a/compare-variants.astro`
+* `src/pages/rsv-a/index.astro`
+* `src/pages/rsv-a/sequencing-efforts.astro`
+* `src/pages/rsv-a/single-variant.astro`
+* `src/pages/rsv-b/compare-side-by-side.astro`
+* `src/pages/rsv-b/compare-to-baseline.astro`
+* `src/pages/rsv-b/compare-variants.astro`
+* `src/pages/rsv-b/index.astro`
+* `src/pages/rsv-b/sequencing-efforts.astro`
+* `src/pages/rsv-b/single-variant.astro`
+* `src/pages/subscriptions/channels/index.astro`
+* `src/pages/subscriptions/create.astro`
+* `src/pages/subscriptions/index.astro`
+* `src/pages/swiss-wastewater/flu.astro`
+* `src/pages/swiss-wastewater/index.astro`
+* `src/pages/swiss-wastewater/rsv.astro`
+* `src/pages/west-nile/compare-side-by-side.astro`
+* `src/pages/west-nile/compare-to-baseline.astro`
+* `src/pages/west-nile/compare-variants.astro`
+* `src/pages/west-nile/index.astro`
+* `src/pages/west-nile/sequencing-efforts.astro`
+* `src/pages/west-nile/single-variant.astro`
+
+## Pages
+
+The filename represents the component name, but is (probably only)
+used via routing directly.
+
+Thus just showing what it *contains* (outputs), not defines.
+
+### errors
+
+* `404.astro`
+* `500.astro`
+
+### covid
+
+* `covid/index.astro`
+
+redirect to 'covid.singleVariantView'
+
+* `covid/compare-side-by-side.astro`
+
+    OrganismViewPageLayout around gs-app but then calling various: CompareSideBySidePageStateSelector CompareSideBySideSelectorFallback GsPrevalenceOverTime GsRelativeGrowthAdvantage GsMutations x 2 GsAggregate x 2
+
+* `covid/compare-to-baseline.astro`
+
+    `<GenericCompareToBaselinePage organism={Organisms.covid} />`
+
+* `covid/compare-variants.astro`
+
+    `<GenericCompareVariantsPage organism={Organisms.covid} />`
+
+* `covid/sequencing-efforts.astro`
+
+    `<GenericSequencingEffortsPage organism={Organisms.covid} />`
+
+* `covid/single-variant.astro`
+
+    SingleVariantOrganismPageLayout, with SelectVariant, GsStatistics, ComponentsGrid { GsPrevalenceOverTime, GsRelativeGrowthAdvantage, GsMutations x 2, GsAggregate x 3 }, GsMutationsOverTime, GsMutationsOverTime
+
+### data
+
+* `data.astro`
+
+    ContaineredPageLayout, PageHeadline, plain HTML with text, "Data sources and preprocessing"
+
+
+### flu
+
+* `flu/compare-side-by-side.astro`
+
+    `<GenericCompareSideBySidePage organism={Organisms.flu} hideMutationComponents={true} />`
+
+* `flu/h5n1/compare-side-by-side.astro`
+* `flu/h5n1/compare-to-baseline.astro`
+* `flu/h5n1/compare-variants.astro`
+* `flu/h5n1/index.astro`
+* `flu/h5n1/sequencing-efforts.astro`
+* `flu/h5n1/single-variant.astro`
+* `flu/index.astro`
+* `flu/sequencing-efforts.astro`
+
+### index, logout
+
+* `index.astro`
+* `logout.astro`
+
+### mpox
+
+* `mpox/compare-side-by-side.astro`
+* `mpox/compare-to-baseline.astro`
+* `mpox/compare-variants.astro`
+* `mpox/index.astro`
+* `mpox/sequencing-efforts.astro`
+* `mpox/single-variant.astro`
+
+### rsv-a
+
+* `rsv-a/compare-side-by-side.astro`
+* `rsv-a/compare-to-baseline.astro`
+* `rsv-a/compare-variants.astro`
+* `rsv-a/index.astro`
+* `rsv-a/sequencing-efforts.astro`
+* `rsv-a/single-variant.astro`
+
+### rsv-b
+
+* `rsv-b/compare-side-by-side.astro`
+* `rsv-b/compare-to-baseline.astro`
+* `rsv-b/compare-variants.astro`
+* `rsv-b/index.astro`
+* `rsv-b/sequencing-efforts.astro`
+* `rsv-b/single-variant.astro`
+
+### subscriptions
+
+* `subscriptions/channels/index.astro`
+* `subscriptions/create.astro`
+* `subscriptions/index.astro`
+
+### swiss-wastewater
+
+* `swiss-wastewater/flu.astro`
+* `swiss-wastewater/index.astro`
+* `swiss-wastewater/rsv.astro`
+
+### west-nile
+
+* `west-nile/compare-side-by-side.astro`
+* `west-nile/compare-to-baseline.astro`
+* `west-nile/compare-variants.astro`
+* `west-nile/index.astro`
+* `west-nile/sequencing-efforts.astro`
+* `west-nile/single-variant.astro`

website/src/types/Organism.ts

@@ -1,3 +1,7 @@
+/**
+ * Identification, basic styling (full name) and page styling information for an organism.
+ */
+
 import { z } from 'zod';
 
 export const Organisms = {

website/src/types/dataOrigins.ts

@@ -1,3 +1,7 @@
+/**
+ * Available data sources for data on an organism
+ */
+
 export const dataOrigins = {
     insdc: 'insdc' as const,
     pathoplexus: 'pathoplexus' as const,

website/src/views/OrganismConstants.ts

@@ -5,9 +5,14 @@ import type { LineageFilterConfig } from '../components/pageStateSelectors/Linea
 import type { Organism } from '../types/Organism.ts';
 import type { DataOrigin } from '../types/dataOrigins.ts';
 
+/**
+ * Organism constants are values describing an organism, that are then used as parameters for setting up
+ * a view for that organism (XX how?).
+ */
 export interface OrganismConstants {
     readonly organism: Organism;
     readonly dataOrigins: DataOrigin[];
+    /** XX what is this? */
     readonly accessionDownloadFields: string[];
 }
 
@@ -16,12 +21,18 @@ export const ComponentHeight = {
     small: '300px',
 } as const;
 
+/**
+ * XX, used in mbox and westNile views
+ */
 export interface AdditionalSequencingEffortsField {
     readonly label: string;
     readonly fields: string[];
     readonly height: (typeof ComponentHeight)[keyof typeof ComponentHeight];
 }
 
+/**
+ * XX, used in all(?) views
+ */
 export interface ExtendedConstants extends OrganismConstants {
     readonly locationFields: string[];
     readonly mainDateField: string;
@@ -36,7 +47,7 @@ export interface ExtendedConstants extends OrganismConstants {
 export function getAuthorRelatedSequencingEffortsFields(constants: {
     authorsField: string | undefined;
     authorAffiliationsField: string | undefined;
-}) {
+}): AdditionalSequencingEffortsField[] {
     const authorAffiliations =
         constants.authorAffiliationsField === undefined
             ? []
@@ -62,7 +73,7 @@ export function getAuthorRelatedSequencingEffortsFields(constants: {
 
 export function getPathoplexusAdditionalSequencingEffortsFields(
     constants: Parameters<typeof getAuthorRelatedSequencingEffortsFields>[0],
-) {
+): AdditionalSequencingEffortsField[] {
     return [
         {
             label: 'Pathoplexus submitting groups',