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feat(web): show what the pipeline is doing while a job runs

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"running" for two and a half minutes tells the user nothing. The job page now shows a
spinner, the elapsed time, and the pipeline step Nextflow is actually on.

- the API streams the Nextflow output into jobs.log as it arrives, instead of keeping it
  only when the run dies. Writes are throttled to one every 3s, or immediately when a new
  process starts, and are skipped for a job that has already finished, so a late line
  cannot overwrite the loader's result.
- web/src/lib/progress.ts formats the elapsed time and picks the latest [PROCESS] line.
  No percentage: the pipeline cannot honestly estimate one.
- the spinner animates only under prefers-reduced-motion: no-preference.

Verified on a live run: the page showed "VEP (tiny)" for the duration, then the variant
table replaced it on success.

Tests: api 53, web 20; ruff, mypy, svelte-check clean.
This commit is contained in:
Kemal Yaylali
2026-09-12 07:46:44 +01:00
parent ae58e33fe2
commit 33e788122b
14 changed files with 638 additions and 13 deletions
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.svelte-kit/ambient.d.ts
Vendored
+360
View File
@@ -0,0 +1,360 @@
// this file is generated — do not edit it
/// <reference types="@sveltejs/kit" />
/**
* This module provides access to environment variables that are injected _statically_ into your bundle at build time and are limited to _private_ access.
*
* | | Runtime | Build time |
* | ------- | -------------------------------------------------------------------------- | ------------------------------------------------------------------------ |
* | Private | [`$env/dynamic/private`](https://svelte.dev/docs/kit/$env-dynamic-private) | [`$env/static/private`](https://svelte.dev/docs/kit/$env-static-private) |
* | Public | [`$env/dynamic/public`](https://svelte.dev/docs/kit/$env-dynamic-public) | [`$env/static/public`](https://svelte.dev/docs/kit/$env-static-public) |
*
* Static environment variables are [loaded by Vite](https://vitejs.dev/guide/env-and-mode.html#env-files) from `.env` files and `process.env` at build time and then statically injected into your bundle at build time, enabling optimisations like dead code elimination.
*
* **_Private_ access:**
*
* - This module cannot be imported into client-side code
* - This module only includes variables that _do not_ begin with [`config.kit.env.publicPrefix`](https://svelte.dev/docs/kit/configuration#env) _and do_ start with [`config.kit.env.privatePrefix`](https://svelte.dev/docs/kit/configuration#env) (if configured)
*
* For example, given the following build time environment:
*
* ```env
* ENVIRONMENT=production
* PUBLIC_BASE_URL=http://site.com
* ```
*
* With the default `publicPrefix` and `privatePrefix`:
*
* ```ts
* import { ENVIRONMENT, PUBLIC_BASE_URL } from '$env/static/private';
*
* console.log(ENVIRONMENT); // => "production"
* console.log(PUBLIC_BASE_URL); // => throws error during build
* ```
*
* The above values will be the same _even if_ different values for `ENVIRONMENT` or `PUBLIC_BASE_URL` are set at runtime, as they are statically replaced in your code with their build time values.
*/
declare module '$env/static/private' {
export const CLAUDE_CODE_MESSAGING_TOKEN: string;
export const NoDefaultCurrentDirectoryInExePath: string;
export const CLAUDE_EFFORT: string;
export const CLAUDE_CODE_ENTRYPOINT: string;
export const VSCODE_CRASH_REPORTER_PROCESS_TYPE: string;
export const NODE: string;
export const INIT_CWD: string;
export const SHELL: string;
export const npm_config_allow_scripts: string;
export const CLAUDE_PID: string;
export const CLAUDE_CODE_CHILD_SESSION: string;
export const TMPDIR: string;
export const HOMEBREW_REPOSITORY: string;
export const npm_config_global_prefix: string;
export const FPATH: string;
export const CLAUDE_AGENT_SDK_VERSION: string;
export const MallocNanoZone: string;
export const COLOR: string;
export const npm_config_noproxy: string;
export const npm_config_local_prefix: string;
export const PNPM_HOME: string;
export const GIT_EDITOR: string;
export const AI_AGENT: string;
export const USER: string;
export const COMMAND_MODE: string;
export const npm_config_globalconfig: string;
export const RAILWAY_HOME: string;
export const SSH_AUTH_SOCK: string;
export const __CF_USER_TEXT_ENCODING: string;
export const npm_execpath: string;
export const ELECTRON_RUN_AS_NODE: string;
export const PATH: string;
export const MCP_CONNECTION_NONBLOCKING: string;
export const npm_package_json: string;
export const _: string;
export const LaunchInstanceID: string;
export const npm_config_userconfig: string;
export const npm_config_init_module: string;
export const __CFBundleIdentifier: string;
export const npm_command: string;
export const PWD: string;
export const VSCODE_HANDLES_UNCAUGHT_ERRORS: string;
export const npm_lifecycle_event: string;
export const EDITOR: string;
export const VSCODE_ESM_ENTRYPOINT: string;
export const npm_package_name: string;
export const LANG: string;
export const npm_config_npm_version: string;
export const XPC_FLAGS: string;
export const MACH_PORT_RENDEZVOUS_PEER_VALDATION: string;
export const npm_config_node_gyp: string;
export const npm_package_version: string;
export const CLAUDE_CODE_ENABLE_TASKS: string;
export const XPC_SERVICE_NAME: string;
export const GEMINI_API_KEY: string;
export const CLAUDE_CODE_ENABLE_SDK_FILE_CHECKPOINTING: string;
export const SHLVL: string;
export const HOME: string;
export const CLAUDE_CODE_EXECPATH: string;
export const VSCODE_NLS_CONFIG: string;
export const APPLICATION_INSIGHTS_NO_STATSBEAT: string;
export const HOMEBREW_PREFIX: string;
export const npm_config_cache: string;
export const LOGNAME: string;
export const npm_lifecycle_script: string;
export const VSCODE_IPC_HOOK: string;
export const VSCODE_CODE_CACHE_PATH: string;
export const COREPACK_ENABLE_AUTO_PIN: string;
export const npm_config_user_agent: string;
export const VSCODE_PID: string;
export const CLAUDE_CODE_SESSION_ID: string;
export const INFOPATH: string;
export const HOMEBREW_CELLAR: string;
export const OSLogRateLimit: string;
export const CLAUDECODE: string;
export const CLAUDE_CODE_MESSAGING_SOCKET: string;
export const VSCODE_L10N_BUNDLE_LOCATION: string;
export const VSCODE_CWD: string;
export const SECURITYSESSIONID: string;
export const npm_node_execpath: string;
export const npm_config_prefix: string;
export const TEST: string;
export const VITEST: string;
export const NODE_ENV: string;
export const PROD: string;
export const DEV: string;
export const BASE_URL: string;
export const MODE: string;
}
/**
* This module provides access to environment variables that are injected _statically_ into your bundle at build time and are _publicly_ accessible.
*
* | | Runtime | Build time |
* | ------- | -------------------------------------------------------------------------- | ------------------------------------------------------------------------ |
* | Private | [`$env/dynamic/private`](https://svelte.dev/docs/kit/$env-dynamic-private) | [`$env/static/private`](https://svelte.dev/docs/kit/$env-static-private) |
* | Public | [`$env/dynamic/public`](https://svelte.dev/docs/kit/$env-dynamic-public) | [`$env/static/public`](https://svelte.dev/docs/kit/$env-static-public) |
*
* Static environment variables are [loaded by Vite](https://vitejs.dev/guide/env-and-mode.html#env-files) from `.env` files and `process.env` at build time and then statically injected into your bundle at build time, enabling optimisations like dead code elimination.
*
* **_Public_ access:**
*
* - This module _can_ be imported into client-side code
* - **Only** variables that begin with [`config.kit.env.publicPrefix`](https://svelte.dev/docs/kit/configuration#env) (which defaults to `PUBLIC_`) are included
*
* For example, given the following build time environment:
*
* ```env
* ENVIRONMENT=production
* PUBLIC_BASE_URL=http://site.com
* ```
*
* With the default `publicPrefix` and `privatePrefix`:
*
* ```ts
* import { ENVIRONMENT, PUBLIC_BASE_URL } from '$env/static/public';
*
* console.log(ENVIRONMENT); // => throws error during build
* console.log(PUBLIC_BASE_URL); // => "http://site.com"
* ```
*
* The above values will be the same _even if_ different values for `ENVIRONMENT` or `PUBLIC_BASE_URL` are set at runtime, as they are statically replaced in your code with their build time values.
*/
declare module '$env/static/public' {
}
/**
* This module provides access to environment variables set _dynamically_ at runtime and that are limited to _private_ access.
*
* | | Runtime | Build time |
* | ------- | -------------------------------------------------------------------------- | ------------------------------------------------------------------------ |
* | Private | [`$env/dynamic/private`](https://svelte.dev/docs/kit/$env-dynamic-private) | [`$env/static/private`](https://svelte.dev/docs/kit/$env-static-private) |
* | Public | [`$env/dynamic/public`](https://svelte.dev/docs/kit/$env-dynamic-public) | [`$env/static/public`](https://svelte.dev/docs/kit/$env-static-public) |
*
* Dynamic environment variables are defined by the platform you're running on. For example if you're using [`adapter-node`](https://github.com/sveltejs/kit/tree/main/packages/adapter-node) (or running [`vite preview`](https://svelte.dev/docs/kit/cli)), this is equivalent to `process.env`.
*
* **_Private_ access:**
*
* - This module cannot be imported into client-side code
* - This module includes variables that _do not_ begin with [`config.kit.env.publicPrefix`](https://svelte.dev/docs/kit/configuration#env) _and do_ start with [`config.kit.env.privatePrefix`](https://svelte.dev/docs/kit/configuration#env) (if configured)
*
* > [!NOTE] In `dev`, `$env/dynamic` includes environment variables from `.env`. In `prod`, this behavior will depend on your adapter.
*
* > [!NOTE] To get correct types, environment variables referenced in your code should be declared (for example in an `.env` file), even if they don't have a value until the app is deployed:
* >
* > ```env
* > MY_FEATURE_FLAG=
* > ```
* >
* > You can override `.env` values from the command line like so:
* >
* > ```sh
* > MY_FEATURE_FLAG="enabled" npm run dev
* > ```
*
* For example, given the following runtime environment:
*
* ```env
* ENVIRONMENT=production
* PUBLIC_BASE_URL=http://site.com
* ```
*
* With the default `publicPrefix` and `privatePrefix`:
*
* ```ts
* import { env } from '$env/dynamic/private';
*
* console.log(env.ENVIRONMENT); // => "production"
* console.log(env.PUBLIC_BASE_URL); // => undefined
* ```
*/
declare module '$env/dynamic/private' {
export const env: {
CLAUDE_CODE_MESSAGING_TOKEN: string;
NoDefaultCurrentDirectoryInExePath: string;
CLAUDE_EFFORT: string;
CLAUDE_CODE_ENTRYPOINT: string;
VSCODE_CRASH_REPORTER_PROCESS_TYPE: string;
NODE: string;
INIT_CWD: string;
SHELL: string;
npm_config_allow_scripts: string;
CLAUDE_PID: string;
CLAUDE_CODE_CHILD_SESSION: string;
TMPDIR: string;
HOMEBREW_REPOSITORY: string;
npm_config_global_prefix: string;
FPATH: string;
CLAUDE_AGENT_SDK_VERSION: string;
MallocNanoZone: string;
COLOR: string;
npm_config_noproxy: string;
npm_config_local_prefix: string;
PNPM_HOME: string;
GIT_EDITOR: string;
AI_AGENT: string;
USER: string;
COMMAND_MODE: string;
npm_config_globalconfig: string;
RAILWAY_HOME: string;
SSH_AUTH_SOCK: string;
__CF_USER_TEXT_ENCODING: string;
npm_execpath: string;
ELECTRON_RUN_AS_NODE: string;
PATH: string;
MCP_CONNECTION_NONBLOCKING: string;
npm_package_json: string;
_: string;
LaunchInstanceID: string;
npm_config_userconfig: string;
npm_config_init_module: string;
__CFBundleIdentifier: string;
npm_command: string;
PWD: string;
VSCODE_HANDLES_UNCAUGHT_ERRORS: string;
npm_lifecycle_event: string;
EDITOR: string;
VSCODE_ESM_ENTRYPOINT: string;
npm_package_name: string;
LANG: string;
npm_config_npm_version: string;
XPC_FLAGS: string;
MACH_PORT_RENDEZVOUS_PEER_VALDATION: string;
npm_config_node_gyp: string;
npm_package_version: string;
CLAUDE_CODE_ENABLE_TASKS: string;
XPC_SERVICE_NAME: string;
GEMINI_API_KEY: string;
CLAUDE_CODE_ENABLE_SDK_FILE_CHECKPOINTING: string;
SHLVL: string;
HOME: string;
CLAUDE_CODE_EXECPATH: string;
VSCODE_NLS_CONFIG: string;
APPLICATION_INSIGHTS_NO_STATSBEAT: string;
HOMEBREW_PREFIX: string;
npm_config_cache: string;
LOGNAME: string;
npm_lifecycle_script: string;
VSCODE_IPC_HOOK: string;
VSCODE_CODE_CACHE_PATH: string;
COREPACK_ENABLE_AUTO_PIN: string;
npm_config_user_agent: string;
VSCODE_PID: string;
CLAUDE_CODE_SESSION_ID: string;
INFOPATH: string;
HOMEBREW_CELLAR: string;
OSLogRateLimit: string;
CLAUDECODE: string;
CLAUDE_CODE_MESSAGING_SOCKET: string;
VSCODE_L10N_BUNDLE_LOCATION: string;
VSCODE_CWD: string;
SECURITYSESSIONID: string;
npm_node_execpath: string;
npm_config_prefix: string;
TEST: string;
VITEST: string;
NODE_ENV: string;
PROD: string;
DEV: string;
BASE_URL: string;
MODE: string;
[key: `PUBLIC_${string}`]: undefined;
[key: `${string}`]: string | undefined;
}
}
/**
* This module provides access to environment variables set _dynamically_ at runtime and that are _publicly_ accessible.
*
* | | Runtime | Build time |
* | ------- | -------------------------------------------------------------------------- | ------------------------------------------------------------------------ |
* | Private | [`$env/dynamic/private`](https://svelte.dev/docs/kit/$env-dynamic-private) | [`$env/static/private`](https://svelte.dev/docs/kit/$env-static-private) |
* | Public | [`$env/dynamic/public`](https://svelte.dev/docs/kit/$env-dynamic-public) | [`$env/static/public`](https://svelte.dev/docs/kit/$env-static-public) |
*
* Dynamic environment variables are defined by the platform you're running on. For example if you're using [`adapter-node`](https://github.com/sveltejs/kit/tree/main/packages/adapter-node) (or running [`vite preview`](https://svelte.dev/docs/kit/cli)), this is equivalent to `process.env`.
*
* **_Public_ access:**
*
* - This module _can_ be imported into client-side code
* - **Only** variables that begin with [`config.kit.env.publicPrefix`](https://svelte.dev/docs/kit/configuration#env) (which defaults to `PUBLIC_`) are included
*
* > [!NOTE] In `dev`, `$env/dynamic` includes environment variables from `.env`. In `prod`, this behavior will depend on your adapter.
*
* > [!NOTE] To get correct types, environment variables referenced in your code should be declared (for example in an `.env` file), even if they don't have a value until the app is deployed:
* >
* > ```env
* > MY_FEATURE_FLAG=
* > ```
* >
* > You can override `.env` values from the command line like so:
* >
* > ```sh
* > MY_FEATURE_FLAG="enabled" npm run dev
* > ```
*
* For example, given the following runtime environment:
*
* ```env
* ENVIRONMENT=production
* PUBLIC_BASE_URL=http://example.com
* ```
*
* With the default `publicPrefix` and `privatePrefix`:
*
* ```ts
* import { env } from '$env/dynamic/public';
* console.log(env.ENVIRONMENT); // => undefined, not public
* console.log(env.PUBLIC_BASE_URL); // => "http://example.com"
* ```
*
* ```
*
* ```
*/
declare module '$env/dynamic/public' {
export const env: {
[key: `PUBLIC_${string}`]: string | undefined;
}
}