feat: migrate from pinia stores to TanStack Query (#247)

.gitignore

@@ -1,3 +1,6 @@
+# log files
+/*.log
+
 # nodejs
 /node_modules
 

Makefile

@@ -110,3 +110,76 @@ proto-ts:
 
 .PHONY: proto
 proto: proto-fetch proto-ts format lint
+
+.PHONY: openapi
+openapi: \
+	openapi-cadaPrio-ts \
+	openapi-dotty-ts \
+	openapi-variantValidator-ts \
+	openapi-viguno-ts \
+	format \
+	lint
+
+.PHONY: openapi-cadaPrio-fetch
+openapi-cadaPrio-fetch:
+	mkdir -p ext/cadaPrio-api
+
+	rm -f ext/cadaPrio-api/openapi.yaml
+	docker pull ghcr.io/bihealth/cada-prio:main
+	docker run ghcr.io/bihealth/cada-prio:main cada-prio utils dump-openapi-yaml /dev/stdout \
+	| grep -v '^+' \
+	> ext/cadaPrio-api/openapi.yaml
+
+.PHONY: openapi-cadaPrio-ts
+openapi-cadaPrio-ts: openapi-cadaPrio-fetch
+	rm -rf ext/cadaPrio-api/src/lib
+	mkdir -p ext/cadaPrio-api/src
+	npx @hey-api/openapi-ts --file openapi-ts.config.cadaPrio.ts
+
+.PHONY: openapi-dotty-fetch
+openapi-dotty-fetch:
+	mkdir -p ext/dotty-api
+
+	rm -f ext/dotty-api/openapi.yaml
+	docker pull ghcr.io/bihealth/dotty:main
+	docker run ghcr.io/bihealth/dotty:main python -m dotty.main \
+	| grep -v '^+' \
+	> ext/dotty-api/openapi.yaml
+
+.PHONY: openapi-dotty-ts
+openapi-dotty-ts: openapi-dotty-fetch
+	rm -rf ext/dotty-api/src/lib
+	mkdir -p ext/dotty-api/src
+	npx @hey-api/openapi-ts --file openapi-ts.config.dotty.ts
+
+.PHONY: openapi-variantValidator-fetch
+openapi-variantValidator-fetch:
+	mkdir -p ext/variantValidator-api
+
+	rm -f ext/variantValidator-api/openapi.yaml
+	wget -O ext/variantValidator-api/openapi.yaml \
+		https://rest.variantvalidator.org/swagger.json
+
+.PHONY: openapi-variantValidator-ts
+openapi-variantValidator-ts: openapi-variantValidator-fetch
+	rm -rf ext/variantValidator-api/src/lib
+	mkdir -p ext/variantValidator-api/src
+	npx @hey-api/openapi-ts --file openapi-ts.config.variantValidator.ts
+
+.PHONY: openapi-viguno-fetch
+openapi-viguno-fetch:
+	rm -rf ext/viguno-api/openapi.yaml
+	mkdir -p ext/viguno-api
+
+	docker pull ghcr.io/varfish-org/viguno:main
+	docker run -t ghcr.io/varfish-org/viguno:main \
+		exec viguno server schema --output-file /dev/stdout \
+	| grep -v ' INFO' \
+	| grep -v '^+' \
+	> ext/viguno-api/openapi.yaml
+
+.PHONY: openapi-viguno-ts
+openapi-viguno-ts: openapi-viguno-fetch
+	rm -rf ext/viguno-api/src/lib
+	mkdir -p ext/viguno-api/src
+	npx @hey-api/openapi-ts --file openapi-ts.config.viguno.ts

ext/cadaPrio-api/openapi.yaml

@@ -0,0 +1,82 @@
+components:
+  schemas:
+    HTTPValidationError:
+      properties:
+        detail:
+          items:
+            $ref: '#/components/schemas/ValidationError'
+          title: Detail
+          type: array
+      title: HTTPValidationError
+      type: object
+    ValidationError:
+      properties:
+        loc:
+          items:
+            anyOf:
+              - type: string
+              - type: integer
+          title: Location
+          type: array
+        msg:
+          title: Message
+          type: string
+        type:
+          title: Error Type
+          type: string
+      required:
+        - loc
+        - msg
+        - type
+      title: ValidationError
+      type: object
+info:
+  description: A phenotype-based gene prioritization tool.
+  title: cada-prio
+  version: 0.6.1
+openapi: 3.1.0
+paths:
+  /api/v1/predict:
+    get:
+      description: Predict genes for a given set of HPO terms and optionally genes.
+      operationId: handle_predict_api_v1_predict_get
+      parameters:
+        - example: HP:0000098,HP:0000218,HP:0000486
+          in: query
+          name: hpo_terms
+          required: true
+          schema:
+            title: Hpo Terms
+            type: string
+        - example: FBN1,TTN,BRCA1
+          in: query
+          name: genes
+          required: false
+          schema:
+            anyOf:
+              - type: string
+              - type: 'null'
+            title: Genes
+      responses:
+        '200':
+          content:
+            application/json:
+              schema: {}
+          description: Successful Response
+        '422':
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPValidationError'
+          description: Validation Error
+      summary: Handle Predict
+  /api/v1/version:
+    get:
+      operationId: version_api_v1_version_get
+      responses:
+        '200':
+          content:
+            application/json:
+              schema: {}
+          description: Successful Response
+      summary: Version

ext/cadaPrio-api/src/lib/@tanstack/vue-query.gen.ts

@@ -0,0 +1,78 @@
+// This file is auto-generated by @hey-api/openapi-ts
+import type { Options } from '@hey-api/client-fetch'
+import { queryOptions } from '@tanstack/vue-query'
+
+import { client, handlePredictApiV1PredictGet, versionApiV1VersionGet } from '../services.gen'
+import type { HandlePredictApiV1PredictGetData } from '../types.gen'
+
+type QueryKey<TOptions extends Options> = [
+  Pick<TOptions, 'baseUrl' | 'body' | 'headers' | 'path' | 'query'> & {
+    _id: string
+    _infinite?: boolean
+  }
+]
+
+const createQueryKey = <TOptions extends Options>(
+  id: string,
+  options?: TOptions,
+  infinite?: boolean
+): QueryKey<TOptions>[0] => {
+  const params: QueryKey<TOptions>[0] = {
+    _id: id,
+    baseUrl: client.getConfig().baseUrl
+  } as QueryKey<TOptions>[0]
+  if (infinite) {
+    params._infinite = infinite
+  }
+  if (options?.body) {
+    params.body = options.body
+  }
+  if (options?.headers) {
+    params.headers = options.headers
+  }
+  if (options?.path) {
+    params.path = options.path
+  }
+  if (options?.query) {
+    params.query = options.query
+  }
+  return params
+}
+
+export const handlePredictApiV1PredictGetQueryKey = (
+  options: Options<HandlePredictApiV1PredictGetData>
+) => [createQueryKey('handlePredictApiV1PredictGet', options)]
+
+export const handlePredictApiV1PredictGetOptions = (
+  options: Options<HandlePredictApiV1PredictGetData>
+) => {
+  return queryOptions({
+    queryFn: async ({ queryKey }) => {
+      const { data } = await handlePredictApiV1PredictGet({
+        ...options,
+        ...queryKey[0],
+        throwOnError: true
+      })
+      return data
+    },
+    queryKey: handlePredictApiV1PredictGetQueryKey(options)
+  })
+}
+
+export const versionApiV1VersionGetQueryKey = (options?: Options) => [
+  createQueryKey('versionApiV1VersionGet', options)
+]
+
+export const versionApiV1VersionGetOptions = (options?: Options) => {
+  return queryOptions({
+    queryFn: async ({ queryKey }) => {
+      const { data } = await versionApiV1VersionGet({
+        ...options,
+        ...queryKey[0],
+        throwOnError: true
+      })
+      return data
+    },
+    queryKey: versionApiV1VersionGetQueryKey(options)
+  })
+}

ext/cadaPrio-api/src/lib/index.ts

@@ -0,0 +1,4 @@
+// This file is auto-generated by @hey-api/openapi-ts
+export * from './schemas.gen'
+export * from './services.gen'
+export * from './types.gen'

ext/cadaPrio-api/src/lib/schemas.gen.ts

@@ -0,0 +1,45 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+export const $HTTPValidationError = {
+  properties: {
+    detail: {
+      items: {
+        $ref: '#/components/schemas/ValidationError'
+      },
+      title: 'Detail',
+      type: 'array'
+    }
+  },
+  title: 'HTTPValidationError',
+  type: 'object'
+} as const
+
+export const $ValidationError = {
+  properties: {
+    loc: {
+      items: {
+        anyOf: [
+          {
+            type: 'string'
+          },
+          {
+            type: 'integer'
+          }
+        ]
+      },
+      title: 'Location',
+      type: 'array'
+    },
+    msg: {
+      title: 'Message',
+      type: 'string'
+    },
+    type: {
+      title: 'Error Type',
+      type: 'string'
+    }
+  },
+  required: ['loc', 'msg', 'type'],
+  title: 'ValidationError',
+  type: 'object'
+} as const

ext/cadaPrio-api/src/lib/services.gen.ts

@@ -0,0 +1,45 @@
+// This file is auto-generated by @hey-api/openapi-ts
+import { type Options, createClient, createConfig } from '@hey-api/client-fetch'
+
+import type {
+  HandlePredictApiV1PredictGetData,
+  HandlePredictApiV1PredictGetError,
+  HandlePredictApiV1PredictGetResponse,
+  VersionApiV1VersionGetError,
+  VersionApiV1VersionGetResponse
+} from './types.gen'
+
+export const client = createClient(createConfig())
+
+/**
+ * Handle Predict
+ * Predict genes for a given set of HPO terms and optionally genes.
+ */
+export const handlePredictApiV1PredictGet = <ThrowOnError extends boolean = false>(
+  options: Options<HandlePredictApiV1PredictGetData, ThrowOnError>
+) => {
+  return (options?.client ?? client).get<
+    HandlePredictApiV1PredictGetResponse,
+    HandlePredictApiV1PredictGetError,
+    ThrowOnError
+  >({
+    ...options,
+    url: '/api/v1/predict'
+  })
+}
+
+/**
+ * Version
+ */
+export const versionApiV1VersionGet = <ThrowOnError extends boolean = false>(
+  options?: Options<unknown, ThrowOnError>
+) => {
+  return (options?.client ?? client).get<
+    VersionApiV1VersionGetResponse,
+    VersionApiV1VersionGetError,
+    ThrowOnError
+  >({
+    ...options,
+    url: '/api/v1/version'
+  })
+}

ext/cadaPrio-api/src/lib/types.gen.ts

@@ -0,0 +1,26 @@
+// This file is auto-generated by @hey-api/openapi-ts
+
+export type HTTPValidationError = {
+  detail?: Array<ValidationError>
+}
+
+export type ValidationError = {
+  loc: Array<string | number>
+  msg: string
+  type: string
+}
+
+export type HandlePredictApiV1PredictGetData = {
+  query: {
+    genes?: string | null
+    hpo_terms: string
+  }
+}
+
+export type HandlePredictApiV1PredictGetResponse = unknown
+
+export type HandlePredictApiV1PredictGetError = HTTPValidationError
+
+export type VersionApiV1VersionGetResponse = unknown
+
+export type VersionApiV1VersionGetError = unknown