feat(web): show what the pipeline is doing while a job runs
"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
Vendored
+360
@@ -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;
|
||||
}
|
||||
}
|
||||
Vendored
+1
@@ -0,0 +1 @@
|
||||
// See https://svelte.dev/docs/kit/environment-variables for more information
|
||||
@@ -0,0 +1,38 @@
|
||||
// in dev, this makes Vite inject its client as this module's first dependency,
|
||||
// so that global constant replacements are installed before any other module
|
||||
// (including user hooks) evaluates. In build it's inert.
|
||||
import.meta.hot;
|
||||
|
||||
|
||||
|
||||
|
||||
export { matchers } from './matchers.js';
|
||||
|
||||
export const nodes = [
|
||||
() => import('./nodes/0'),
|
||||
() => import('./nodes/1')
|
||||
];
|
||||
|
||||
export const server_loads = [];
|
||||
|
||||
export const dictionary = {
|
||||
|
||||
};
|
||||
|
||||
export const hooks = {
|
||||
handleError: (({ error }) => { console.error(error) }),
|
||||
|
||||
reroute: (() => {}),
|
||||
transport: {}
|
||||
};
|
||||
|
||||
export const decoders = Object.fromEntries(Object.entries(hooks.transport).map(([k, v]) => [k, v.decode]));
|
||||
export const encoders = Object.fromEntries(Object.entries(hooks.transport).map(([k, v]) => [k, v.encode]));
|
||||
|
||||
export const hash = false;
|
||||
|
||||
export const decode = (type, value) => decoders[type](value);
|
||||
|
||||
export { default as root } from '../root.js';
|
||||
|
||||
export const get_error_template = () => import('../shared/error-template.js').then(m => m.default);
|
||||
@@ -0,0 +1 @@
|
||||
export const matchers = {};
|
||||
@@ -0,0 +1 @@
|
||||
export { default as component } from "../../../../web/node_modules/@sveltejs/kit/src/runtime/components/svelte-5/layout.svelte";
|
||||
@@ -0,0 +1 @@
|
||||
export { default as component } from "../../../../web/node_modules/@sveltejs/kit/src/runtime/components/svelte-5/error.svelte";
|
||||
@@ -0,0 +1 @@
|
||||
export default ({ status, message }) => "<!doctype html>\n<html lang=\"en\">\n\t<head>\n\t\t<meta charset=\"utf-8\" />\n\t\t<title>" + message + "</title>\n\n\t\t<style>\n\t\t\tbody {\n\t\t\t\t--bg: white;\n\t\t\t\t--fg: #222;\n\t\t\t\t--divider: #ccc;\n\t\t\t\tbackground: var(--bg);\n\t\t\t\tcolor: var(--fg);\n\t\t\t\tfont-family:\n\t\t\t\t\tsystem-ui,\n\t\t\t\t\t-apple-system,\n\t\t\t\t\tBlinkMacSystemFont,\n\t\t\t\t\t'Segoe UI',\n\t\t\t\t\tRoboto,\n\t\t\t\t\tOxygen,\n\t\t\t\t\tUbuntu,\n\t\t\t\t\tCantarell,\n\t\t\t\t\t'Open Sans',\n\t\t\t\t\t'Helvetica Neue',\n\t\t\t\t\tsans-serif;\n\t\t\t\tdisplay: flex;\n\t\t\t\talign-items: center;\n\t\t\t\tjustify-content: center;\n\t\t\t\theight: 100vh;\n\t\t\t\tmargin: 0;\n\t\t\t}\n\n\t\t\t.error {\n\t\t\t\tdisplay: flex;\n\t\t\t\talign-items: center;\n\t\t\t\tmax-width: 32rem;\n\t\t\t\tmargin: 0 1rem;\n\t\t\t}\n\n\t\t\t.status {\n\t\t\t\tfont-weight: 200;\n\t\t\t\tfont-size: 3rem;\n\t\t\t\tline-height: 1;\n\t\t\t\tposition: relative;\n\t\t\t\ttop: -0.05rem;\n\t\t\t}\n\n\t\t\t.message {\n\t\t\t\tborder-left: 1px solid var(--divider);\n\t\t\t\tpadding: 0 0 0 1rem;\n\t\t\t\tmargin: 0 0 0 1rem;\n\t\t\t\tmin-height: 2.5rem;\n\t\t\t\tdisplay: flex;\n\t\t\t\talign-items: center;\n\t\t\t}\n\n\t\t\t.message h1 {\n\t\t\t\tfont-weight: 400;\n\t\t\t\tfont-size: 1em;\n\t\t\t\tmargin: 0;\n\t\t\t}\n\n\t\t\t@media (prefers-color-scheme: dark) {\n\t\t\t\tbody {\n\t\t\t\t\t--bg: #222;\n\t\t\t\t\t--fg: #ddd;\n\t\t\t\t\t--divider: #666;\n\t\t\t\t}\n\t\t\t}\n\t\t</style>\n\t</head>\n\t<body>\n\t\t<div class=\"error\">\n\t\t\t<span class=\"status\">" + status + "</span>\n\t\t\t<div class=\"message\">\n\t\t\t\t<h1>" + message + "</h1>\n\t\t\t</div>\n\t\t</div>\n\t</body>\n</html>\n";
|
||||
@@ -0,0 +1,50 @@
|
||||
{
|
||||
"compilerOptions": {
|
||||
"paths": {
|
||||
"$app/types": [
|
||||
"./types/index.d.ts"
|
||||
]
|
||||
},
|
||||
"rootDirs": [
|
||||
"..",
|
||||
"./types"
|
||||
],
|
||||
"verbatimModuleSyntax": true,
|
||||
"isolatedModules": true,
|
||||
"lib": [
|
||||
"esnext",
|
||||
"DOM",
|
||||
"DOM.Iterable"
|
||||
],
|
||||
"moduleResolution": "bundler",
|
||||
"module": "esnext",
|
||||
"noEmit": true,
|
||||
"target": "esnext"
|
||||
},
|
||||
"include": [
|
||||
"ambient.d.ts",
|
||||
"env.d.ts",
|
||||
"non-ambient.d.ts",
|
||||
"./types/**/$types.d.ts",
|
||||
"../vite.config.js",
|
||||
"../vite.config.ts",
|
||||
"../src/**/*.js",
|
||||
"../src/**/*.ts",
|
||||
"../src/**/*.svelte",
|
||||
"../test/**/*.js",
|
||||
"../test/**/*.ts",
|
||||
"../test/**/*.svelte",
|
||||
"../tests/**/*.js",
|
||||
"../tests/**/*.ts",
|
||||
"../tests/**/*.svelte"
|
||||
],
|
||||
"exclude": [
|
||||
"../node_modules/**",
|
||||
"../src/service-worker.js",
|
||||
"../src/service-worker/**/*.js",
|
||||
"../src/service-worker.ts",
|
||||
"../src/service-worker/**/*.ts",
|
||||
"../src/service-worker.d.ts",
|
||||
"../src/service-worker/**/*.d.ts"
|
||||
]
|
||||
}
|
||||
@@ -12,11 +12,15 @@ import json
|
||||
import logging
|
||||
import os
|
||||
import shutil
|
||||
import time
|
||||
import uuid
|
||||
from collections import deque
|
||||
from datetime import UTC, datetime
|
||||
from functools import cache
|
||||
from typing import Any
|
||||
|
||||
from sqlalchemy import update
|
||||
|
||||
from app.config import settings
|
||||
from app.db import SessionLocal
|
||||
from app.models import Job, JobStatus
|
||||
@@ -24,7 +28,8 @@ from app.models import Job, JobStatus
|
||||
logger = logging.getLogger(__name__)
|
||||
|
||||
PIPELINE_ENTRYPOINT = "/pipeline/main.nf"
|
||||
LOG_TAIL_CHARS = 4000
|
||||
PROGRESS_LINES = 12 # rolling window of pipeline output kept on the job
|
||||
PROGRESS_INTERVAL_S = 3 # between writes, unless a new process starts
|
||||
PUBLISH_TIMEOUT_S = 30
|
||||
_watchers: set[asyncio.Task[None]] = set()
|
||||
|
||||
@@ -129,14 +134,36 @@ async def _run_local(job_id: uuid.UUID, vcf_uri: str, assembly: str) -> str:
|
||||
|
||||
|
||||
async def _watch(job_id: uuid.UUID, proc: Any) -> None:
|
||||
out, err = await proc.communicate()
|
||||
if proc.returncode == 0:
|
||||
"""Follow the pipeline: record progress while it runs, and the reason if it dies."""
|
||||
tail: deque[str] = deque(maxlen=PROGRESS_LINES)
|
||||
last_write = 0.0
|
||||
if proc.stdout is not None: # stderr is merged into stdout
|
||||
async for raw in proc.stdout:
|
||||
line = raw.decode(errors="replace").rstrip()
|
||||
if not line:
|
||||
continue
|
||||
tail.append(line)
|
||||
now = time.monotonic()
|
||||
# A new pipeline step is worth showing at once; otherwise throttle the writes.
|
||||
if line.startswith("[PROCESS") or now - last_write >= PROGRESS_INTERVAL_S:
|
||||
last_write = now
|
||||
await _record_progress(job_id, "\n".join(tail))
|
||||
returncode = await proc.wait()
|
||||
if returncode == 0:
|
||||
return # the loader marks the job succeeded
|
||||
tail = ((out or b"") + (err or b"")).decode(errors="replace")[-LOG_TAIL_CHARS:]
|
||||
async with SessionLocal() as session:
|
||||
job = await session.get(Job, job_id)
|
||||
if job is not None and job.status != JobStatus.succeeded:
|
||||
job.status = JobStatus.failed
|
||||
job.log = f"nextflow exited with code {proc.returncode}\n{tail}"
|
||||
job.log = f"nextflow exited with code {returncode}\n" + "\n".join(tail)
|
||||
job.finished_at = datetime.now(UTC)
|
||||
await session.commit()
|
||||
|
||||
|
||||
async def _record_progress(job_id: uuid.UUID, text: str) -> None:
|
||||
"""Put the latest output on the job, leaving a job that has already finished alone."""
|
||||
async with SessionLocal() as session:
|
||||
await session.execute(
|
||||
update(Job).where(Job.id == job_id, Job.status == JobStatus.running).values(log=text)
|
||||
)
|
||||
await session.commit()
|
||||
|
||||
@@ -33,14 +33,29 @@ async def test_local_without_nextflow_fails_fast_with_instructions(
|
||||
assert job["finished_at"] is not None
|
||||
|
||||
|
||||
class FakeProcess:
|
||||
def __init__(self, returncode: int, stderr: bytes) -> None:
|
||||
self.returncode = returncode
|
||||
self._stderr = stderr
|
||||
self.pid = 4242
|
||||
class FakeStdout:
|
||||
"""Stands in for asyncio's StreamReader: async-iterates the process output."""
|
||||
|
||||
async def communicate(self) -> tuple[bytes, bytes]:
|
||||
return b"", self._stderr
|
||||
def __init__(self, lines: list[bytes]) -> None:
|
||||
self._lines = lines
|
||||
|
||||
def __aiter__(self) -> "FakeStdout":
|
||||
return self
|
||||
|
||||
async def __anext__(self) -> bytes:
|
||||
if not self._lines:
|
||||
raise StopAsyncIteration
|
||||
return self._lines.pop(0)
|
||||
|
||||
|
||||
class FakeProcess:
|
||||
def __init__(self, returncode: int, output: bytes = b"", lines: list[bytes] | None = None) -> None:
|
||||
self.returncode = returncode
|
||||
self.pid = 4242
|
||||
self.stdout = FakeStdout(lines if lines is not None else ([output] if output else []))
|
||||
|
||||
async def wait(self) -> int:
|
||||
return self.returncode
|
||||
|
||||
|
||||
@pytest.mark.usefixtures("db")
|
||||
@@ -149,3 +164,49 @@ async def test_the_pipeline_gets_its_own_database_url(
|
||||
await client.post(f"/api/samples/{sample_id}/annotate")
|
||||
await events.drain()
|
||||
assert launched["env"]["DATABASE_URL"] == "postgresql+asyncpg://u:[email protected]:5432/db"
|
||||
|
||||
|
||||
@pytest.mark.usefixtures("db")
|
||||
async def test_progress_is_recorded_while_the_pipeline_runs(
|
||||
client: AsyncClient, monkeypatch: pytest.MonkeyPatch
|
||||
) -> None:
|
||||
"""The UI needs something better than "running" for two minutes."""
|
||||
monkeypatch.setattr(settings, "pubsub_topic", None)
|
||||
monkeypatch.setattr(settings, "cloudrun_job", None)
|
||||
monkeypatch.setattr(events.shutil, "which", lambda _: "/usr/bin/nextflow")
|
||||
|
||||
async def fake_exec(*cmd: str, **kw: Any) -> FakeProcess:
|
||||
return FakeProcess(0, lines=[
|
||||
b"[PIPELINE] main.nf | profile=docker\n",
|
||||
b"[PROCESS f2/5c13bd] NORMALISE (tiny)\n",
|
||||
b"[PROCESS cc/d62082] VEP (tiny)\n",
|
||||
])
|
||||
|
||||
monkeypatch.setattr(events.asyncio, "create_subprocess_exec", fake_exec)
|
||||
sample_id = await new_sample(client)
|
||||
|
||||
r = await client.post(f"/api/samples/{sample_id}/annotate")
|
||||
await events.drain()
|
||||
|
||||
job = (await client.get(f"/api/jobs/{r.json()['id']}")).json()
|
||||
assert "VEP (tiny)" in job["log"]
|
||||
assert job["status"] == "running" # the loader is what marks it succeeded
|
||||
|
||||
|
||||
@pytest.mark.usefixtures("db")
|
||||
async def test_progress_never_overwrites_a_finished_job(client: AsyncClient) -> None:
|
||||
from app.db import SessionLocal
|
||||
from app.models import Job, JobStatus, Sample
|
||||
|
||||
async with SessionLocal() as s:
|
||||
sample = Sample(name=f"s-{uuid.uuid4()}", vcf_uri="gs://b/x.vcf.gz", assembly="GRCh38")
|
||||
job = Job(sample=sample, status=JobStatus.succeeded)
|
||||
s.add_all([sample, job])
|
||||
await s.commit()
|
||||
job_id = job.id
|
||||
|
||||
await events._record_progress(job_id, "[PROCESS 1/a] VEP (late)")
|
||||
|
||||
job_json = (await client.get(f"/api/jobs/{job_id}")).json()
|
||||
assert job_json["status"] == "succeeded"
|
||||
assert job_json["log"] is None
|
||||
|
||||
+8
-1
@@ -32,4 +32,11 @@ td.coord, td.hgvs { font-family: var(--mono); font-size: 0.85rem; } /* aligned
|
||||
.status { font-weight: 600; }
|
||||
.status.failed { color: #9a1b1b; }
|
||||
.status.running, .status.queued { color: var(--amber); }
|
||||
@media (prefers-reduced-motion: no-preference) { button { transition: background 120ms; } }
|
||||
.progress { display: flex; align-items: center; gap: 0.6rem; color: var(--ink-soft); margin: 0.25rem 0 1rem; }
|
||||
.progress .hgvs { font-size: 0.85rem; }
|
||||
.spinner { width: 0.9rem; height: 0.9rem; flex: none; border: 2px solid var(--line); border-top-color: var(--plum); border-radius: 50%; }
|
||||
@media (prefers-reduced-motion: no-preference) {
|
||||
button { transition: background 120ms; }
|
||||
.spinner { animation: spin 0.9s linear infinite; }
|
||||
}
|
||||
@keyframes spin { to { transform: rotate(360deg); } }
|
||||
|
||||
@@ -0,0 +1,34 @@
|
||||
import { describe, expect, it } from 'vitest';
|
||||
import { formatElapsed, latestStep } from './progress';
|
||||
|
||||
describe('formatElapsed', () => {
|
||||
it('shows seconds under a minute', () => expect(formatElapsed(9_000)).toBe('9s'));
|
||||
it('pads the seconds past a minute', () => expect(formatElapsed(64_000)).toBe('1m 04s'));
|
||||
it('drops to minutes past an hour', () => expect(formatElapsed(3_725_000)).toBe('1h 02m'));
|
||||
it('never goes negative when the clocks disagree', () => expect(formatElapsed(-5_000)).toBe('0s'));
|
||||
});
|
||||
|
||||
describe('latestStep', () => {
|
||||
it('names the process Nextflow is on', () => {
|
||||
const log = [
|
||||
'[PIPELINE] main.nf | profile=docker',
|
||||
'[WORKDIR] /x/work',
|
||||
'[PROCESS f2/5c13bd] NORMALISE (tiny)',
|
||||
'[PROCESS cc/d62082] VEP (tiny)'
|
||||
].join('\n');
|
||||
expect(latestStep(log)).toBe('VEP (tiny)');
|
||||
});
|
||||
|
||||
it('falls back to the last meaningful line', () => {
|
||||
expect(latestStep('pulling ensemblorg/ensembl-vep\n\n')).toBe('pulling ensemblorg/ensembl-vep');
|
||||
});
|
||||
|
||||
it('has nothing to say before the first line arrives', () => {
|
||||
expect(latestStep(null)).toBeNull();
|
||||
expect(latestStep(' \n\n')).toBeNull();
|
||||
});
|
||||
|
||||
it('truncates a runaway line', () => {
|
||||
expect(latestStep('x'.repeat(300))!.length).toBeLessThanOrEqual(120);
|
||||
});
|
||||
});
|
||||
@@ -0,0 +1,24 @@
|
||||
const MAX_STEP_CHARS = 120;
|
||||
|
||||
/** "9s", "1m 04s", "1h 02m". How long it has been going, not a made-up percentage. */
|
||||
export function formatElapsed(ms: number): string {
|
||||
const total = Math.max(0, Math.floor(ms / 1000));
|
||||
const hours = Math.floor(total / 3600);
|
||||
const minutes = Math.floor((total % 3600) / 60);
|
||||
const seconds = total % 60;
|
||||
if (hours) return `${hours}h ${String(minutes).padStart(2, '0')}m`;
|
||||
if (minutes) return `${minutes}m ${String(seconds).padStart(2, '0')}s`;
|
||||
return `${seconds}s`;
|
||||
}
|
||||
|
||||
/** The pipeline step Nextflow last started, else the last line it printed. */
|
||||
export function latestStep(log: string | null): string | null {
|
||||
const lines = (log ?? '')
|
||||
.split('\n')
|
||||
.map((line) => line.trim())
|
||||
.filter(Boolean);
|
||||
if (lines.length === 0) return null;
|
||||
const started = [...lines].reverse().find((line) => line.startsWith('[PROCESS'));
|
||||
const step = started ? started.replace(/^\[PROCESS [^\]]*\]\s*/, '') : lines[lines.length - 1];
|
||||
return step.slice(0, MAX_STEP_CHARS);
|
||||
}
|
||||
@@ -2,6 +2,7 @@
|
||||
import { onDestroy, onMount } from 'svelte';
|
||||
import { api, type Job, type VariantPage } from '$lib/api';
|
||||
import { poll } from '$lib/poll';
|
||||
import { formatElapsed, latestStep } from '$lib/progress';
|
||||
|
||||
const POLL_MS = 3000;
|
||||
const finished = (j: Job) => j.status === 'succeeded' || j.status === 'failed';
|
||||
@@ -15,6 +16,18 @@
|
||||
let busy = $state(false);
|
||||
let error = $state<string | null>(null);
|
||||
let stopPolling: (() => void) | null = null;
|
||||
let now = $state(Date.now());
|
||||
|
||||
const running = $derived(!!job && !finished(job));
|
||||
const elapsedMs = $derived(job ? now - Date.parse(job.created_at) : 0);
|
||||
const step = $derived(latestStep(job?.log ?? null));
|
||||
|
||||
// Tick the elapsed time while a run is in flight; polling refreshes the step itself.
|
||||
$effect(() => {
|
||||
if (!running) return;
|
||||
const tick = setInterval(() => (now = Date.now()), 1000);
|
||||
return () => clearInterval(tick);
|
||||
});
|
||||
|
||||
onMount(async () => {
|
||||
try {
|
||||
@@ -79,6 +92,12 @@
|
||||
|
||||
{#if job}
|
||||
<p>Job <span class="hgvs">{job.id.slice(0, 8)}</span>: <span class="status {job.status}">{job.status}</span></p>
|
||||
{#if running}
|
||||
<p class="progress" aria-live="polite">
|
||||
<span class="spinner" aria-hidden="true"></span>
|
||||
Annotating for {formatElapsed(elapsedMs)}{#if step} · <span class="hgvs">{step}</span>{/if}
|
||||
</p>
|
||||
{/if}
|
||||
{#if job.status === 'failed' && job.log}
|
||||
<pre class="hgvs" style="white-space:pre-wrap; background:white; border:1px solid var(--line); padding:0.75rem; max-height:16rem; overflow:auto">{job.log}</pre>
|
||||
{/if}
|
||||
|
||||
Reference in New Issue
Block a user