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"integrity": "sha512-AyFQ0EVmsOZOlAnxoFOGOq1SQDWAB7C6aqMGS23svWAllfOaxbuFvcT8D1i8z3Gyn8fraVeZNNmN6e9bxxXkKw==", + "dev": true + }, "node_modules/web-namespaces": { "version": "2.0.1", "resolved": "https://registry.npmjs.org/web-namespaces/-/web-namespaces-2.0.1.tgz", @@ -10764,6 +11388,15 @@ "node": ">=0.4" } }, + "node_modules/y18n": { + "version": "5.0.8", + "resolved": "https://registry.npmjs.org/y18n/-/y18n-5.0.8.tgz", + "integrity": "sha512-0pfFzegeDWJHJIAmTLRP2DwHjdF5s7jo9tuztdQxAhINCdvS+3nGINqPd00AphqJR/0LhANUS6/+7SCb98YOfA==", + "dev": true, + "engines": { + "node": ">=10" + } + }, "node_modules/yallist": { "version": "3.1.1", "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.1.1.tgz", @@ -10777,6 +11410,24 @@ "node": ">= 14" } }, + "node_modules/yargs": { + "version": "17.7.2", + "resolved": "https://registry.npmjs.org/yargs/-/yargs-17.7.2.tgz", + "integrity": "sha512-7dSzzRQ++CKnNI/krKnYRV7JKKPUXMEh61soaHKg9mrWEhzFWhFnxPxGl+69cD1Ou63C13NUPCnmIcrvqCuM6w==", + "dev": true, + "dependencies": { + "cliui": "^8.0.1", + "escalade": "^3.1.1", + "get-caller-file": "^2.0.5", + "require-directory": "^2.1.1", + "string-width": "^4.2.3", + "y18n": "^5.0.5", + "yargs-parser": "^21.1.1" + }, + "engines": { + "node": ">=12" + } + }, "node_modules/yargs-parser": { "version": "21.1.1", "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-21.1.1.tgz", @@ -10785,6 +11436,47 @@ "node": ">=12" } }, + "node_modules/yargs/node_modules/ansi-regex": { + "version": "5.0.1", + "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-5.0.1.tgz", + "integrity": "sha512-quJQXlTSUGL2LH9SUXo8VwsY4soanhgo6LNSm84E1LBcE8s3O0wpdiRzyR9z/ZZJMlMWv37qOOb9pdJlMUEKFQ==", + "dev": true, + "engines": { + "node": ">=8" + } + }, + "node_modules/yargs/node_modules/emoji-regex": { + "version": "8.0.0", + "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz", + "integrity": 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"https://registry.npmjs.org/yocto-queue/-/yocto-queue-1.0.0.tgz", diff --git a/lapis2-docs/package.json b/lapis2-docs/package.json index 6cd8c0937..5ec54afab 100644 --- a/lapis2-docs/package.json +++ b/lapis2-docs/package.json @@ -9,7 +9,8 @@ "preview": "astro preview", "astro": "astro", "check-format": "prettier --check \"**/*.{ts,tsx,json,astro,md,mdx,mjs,cjs}\"", - "format": "prettier --write \"**/*.{ts,tsx,json,astro,md,mdx,mjs,cjs}\"" + "format": "prettier --write \"**/*.{ts,tsx,json,astro,md,mdx,mjs,cjs}\"", + "check-types": "tsc --noEmit && CONFIG_FILE=../siloLapisTests/testData/testDatabaseConfig.yaml astro check" }, "dependencies": { "@astrojs/react": "^3.0.7", @@ -29,8 +30,10 @@ "yaml": "^2.3.4" }, "devDependencies": { - "@types/swagger-ui": "^3.52.3", + "@astrojs/check": "^0.3.2", + "@types/swagger-ui": "^3.52.4", "prettier": "^3.0.0", - "prettier-plugin-astro": "^0.12.1" + "prettier-plugin-astro": "^0.12.1", + "typescript": "^5.3.3" } } diff --git a/lapis2-docs/src/components/QueryGenerator/LabelledInput.tsx b/lapis2-docs/src/components/QueryGenerator/LabelledInput.tsx new file mode 100644 index 000000000..6f78204dd --- /dev/null +++ b/lapis2-docs/src/components/QueryGenerator/LabelledInput.tsx @@ -0,0 +1,19 @@ +type Props = { + label: string; + value: string | number | undefined; + onChange: (value: string) => void; +}; + +export const LabelledInput = ({ label, value, onChange }: Props) => { + return ( +
+ + onChange(e.target.value)} + /> +
+ ); +}; diff --git a/lapis2-docs/src/components/QueryGenerator/OrderLimitOffsetSelection.tsx b/lapis2-docs/src/components/QueryGenerator/OrderLimitOffsetSelection.tsx new file mode 100644 index 000000000..812d4e9e8 --- /dev/null +++ b/lapis2-docs/src/components/QueryGenerator/OrderLimitOffsetSelection.tsx @@ -0,0 +1,80 @@ +import type { Config } from '../../config.ts'; +import type { Dispatch, SetStateAction } from 'react'; +import type { Selection } from './QueryTypeSelection.tsx'; +import { LabelledInput } from './LabelledInput.tsx'; + +export type OrderByLimitOffset = { + orderBy: string[] | undefined; + limit: number | undefined; + offset: number | undefined; +}; + +type Props = { + config: Config; + selection: Selection; + orderByLimitOffset: OrderByLimitOffset; + onOrderByLimitOffsetChange: Dispatch>; +}; + +export const OrderLimitOffsetSelection = ({ config, orderByLimitOffset, onOrderByLimitOffsetChange }: Props) => { + return ( +
+ {JSON.stringify(orderByLimitOffset)} +
+ +
+ {orderByLimitOffset.orderBy?.map((value, index) => ( +
+ + onOrderByLimitOffsetChange((prev) => ({ + ...prev, + orderBy: prev.orderBy?.map((v, i) => (i === index ? e.target.value : v)), + })) + } + /> + +
+ ))} + + +
+
+ + onOrderByLimitOffsetChange((prev) => ({ + ...prev, + limit: value === '' ? undefined : parseInt(value), + })) + } + /> + + onOrderByLimitOffsetChange((prev) => ({ + ...prev, + offset: value === '' ? undefined : parseInt(value), + })) + } + /> +
+ ); +}; diff --git a/lapis2-docs/src/components/QueryGenerator/QueryGenerator.tsx b/lapis2-docs/src/components/QueryGenerator/QueryGenerator.tsx index b5e16c22f..83ccb3325 100644 --- a/lapis2-docs/src/components/QueryGenerator/QueryGenerator.tsx +++ b/lapis2-docs/src/components/QueryGenerator/QueryGenerator.tsx @@ -1,8 +1,9 @@ import { useState } from 'react'; -import { QueryTypeSelection, type QueryTypeSelectionState } from './QueryTypeSelection'; +import { QueryTypeSelection, type QueryTypeSelectionState, type WithResponseFields } from './QueryTypeSelection'; import { type Filters, FiltersSelection } from './FiltersSelection'; import { Result } from './Result'; import type { Config } from '../../config'; +import { type OrderByLimitOffset, OrderLimitOffsetSelection } from './OrderLimitOffsetSelection.tsx'; type Props = { config: Config; @@ -11,31 +12,13 @@ type Props = { export const QueryGenerator = ({ config, lapisUrl }: Props) => { const [step, setStep] = useState(0); - const [queryType, setQueryType] = useState({ - selection: 'aggregatedAll', - aggregatedAll: {}, - aggregatedStratified: { - fields: new Set(), - }, - mutations: { - type: 'nucleotide', - minProportion: '0.05', - }, - insertions: { - type: 'nucleotide', - }, - details: { - type: 'all', - fields: new Set(), - }, - nucleotideSequences: { - type: 'unaligned', - }, - aminoAcidSequences: { - gene: '', - }, - }); + const [queryType, setQueryType] = useState(getInitialQueryState(config)); const [filters, setFilters] = useState(new Map()); + const [orderByLimitOffset, setOrderByLimitOffset] = useState({ + orderBy: undefined, + limit: undefined, + offset: undefined, + }); return (
@@ -51,7 +34,14 @@ export const QueryGenerator = ({ config, lapisUrl }: Props) => {
{step === 0 && } {step === 1 && } - {step === 2 && <>TODO} + {step === 2 && ( + + )} {step === 3 && }
@@ -66,3 +56,62 @@ export const QueryGenerator = ({ config, lapisUrl }: Props) => {
); }; + +function getInitialQueryState(config: Config): QueryTypeSelectionState { + return { + selection: 'aggregatedAll', + aggregatedAll: {}, + aggregatedStratified: withResponseFields( + { + fields: new Set(), + }, + ['count'], + ), + mutations: withResponseFields( + { + type: 'nucleotide', + minProportion: '0.05', + }, + ['mutation', 'proportion', 'count'], + ), + insertions: withResponseFields( + { + type: 'nucleotide', + }, + ['insertion', 'count'], + ), + details: withResponseFields( + { + type: 'all', + fields: new Set(), + }, + [], + ), + nucleotideSequences: withResponseFields( + { + type: 'unaligned', + }, + [], + ), + aminoAcidSequences: withResponseFields( + { + gene: '', + }, + [], + ), + }; +} + +function withResponseFields< + A extends { + fields?: Set; + } & Record, +>(initialObject: A, fieldsThatAreAlwaysPresent: string[]): WithResponseFields { + return { + ...initialObject, + getResponseFields: () => [ + ...fieldsThatAreAlwaysPresent, + ...(initialObject.fields ? [...initialObject.fields] : []), + ], + }; +} diff --git a/lapis2-docs/src/components/QueryGenerator/QueryTypeSelection.tsx b/lapis2-docs/src/components/QueryGenerator/QueryTypeSelection.tsx index 513972d50..1598faa07 100644 --- a/lapis2-docs/src/components/QueryGenerator/QueryTypeSelection.tsx +++ b/lapis2-docs/src/components/QueryGenerator/QueryTypeSelection.tsx @@ -2,14 +2,7 @@ import type { ReactNode } from 'react'; import type { Config } from '../../config'; import { CheckBoxesWrapper, ContainerWrapper, LabeledCheckBox, LabelWrapper } from './styled-components'; -type Selection = - | 'aggregatedAll' - | 'aggregatedStratified' - | 'mutations' - | 'insertions' - | 'details' - | 'nucleotideSequences' - | 'aminoAcidSequences'; +export type Selection = keyof Omit; const sequenceTypes = ['nucleotide', 'aminoAcid'] as const; type SequenceType = (typeof sequenceTypes)[number]; @@ -20,28 +13,30 @@ type AlignmentType = (typeof alignmentTypes)[number]; export type QueryTypeSelectionState = { selection: Selection; aggregatedAll: {}; - aggregatedStratified: { + aggregatedStratified: WithResponseFields<{ fields: Set; - }; - mutations: { + }>; + mutations: WithResponseFields<{ type: SequenceType; minProportion: string; - }; - insertions: { + }>; + insertions: WithResponseFields<{ type: SequenceType; - }; - details: { + }>; + details: WithResponseFields<{ type: DetailsType; fields: Set; - }; - nucleotideSequences: { + }>; + nucleotideSequences: WithResponseFields<{ type: AlignmentType; - }; - aminoAcidSequences: { + }>; + aminoAcidSequences: WithResponseFields<{ gene: string; - }; + }>; }; +export type WithResponseFields = { getResponseFields: () => string[] } & T; + type Props = { config: Config; state: QueryTypeSelectionState; diff --git a/lapis2-docs/src/components/TabsBox/astro/rehype-tabs.ts b/lapis2-docs/src/components/TabsBox/astro/rehype-tabs.ts index 5052adac8..34dedeae3 100644 --- a/lapis2-docs/src/components/TabsBox/astro/rehype-tabs.ts +++ b/lapis2-docs/src/components/TabsBox/astro/rehype-tabs.ts @@ -1,3 +1,5 @@ +// @ts-nocheck + // This code is largely based/copied from // https://github.com/withastro/starlight/tree/6c387705f1019466ad177355d78eb25f58d928ec/packages/starlight/user-components import { select } from 'hast-util-select'; diff --git a/lapis2-docs/src/components/TabsBox/react/TabsBox.tsx b/lapis2-docs/src/components/TabsBox/react/TabsBox.tsx index 4db206e1d..574e7ca87 100644 --- a/lapis2-docs/src/components/TabsBox/react/TabsBox.tsx +++ b/lapis2-docs/src/components/TabsBox/react/TabsBox.tsx @@ -1,4 +1,4 @@ -import React, { FC, ReactElement, ReactNode, useState } from 'react'; +import React, { type FC, type ReactElement, type ReactNode, useState } from 'react'; type Props = { children: React.ReactNode; diff --git a/lapis2-docs/src/content/docs/getting-started/introduction.mdx b/lapis2-docs/src/content/docs/getting-started/introduction.mdx index 5f37b0963..e9daeb977 100644 --- a/lapis2-docs/src/content/docs/getting-started/introduction.mdx +++ b/lapis2-docs/src/content/docs/getting-started/introduction.mdx @@ -22,6 +22,9 @@ to answer genomic epidemiological questions. Main features include: To get started, you can use our [**interactive wizard**](../generate-your-request/) to generate your query. We provide code examples for Python and R. +LAPIS is open source and available on [GitHub](https://github.com/GenSpectrum/LAPIS). +Feel free to report any issues there. Contributions are welcome. + You can find background information of LAPIS in the following publication. For up-to-date information, please rely on this documentation.