diff --git a/.svelte-kit/ambient.d.ts b/.svelte-kit/ambient.d.ts
new file mode 100644
index 0000000..701a06a
--- /dev/null
+++ b/.svelte-kit/ambient.d.ts
@@ -0,0 +1,360 @@
+
+// this file is generated — do not edit it
+
+
+///
+
+/**
+ * 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;
+ }
+}
diff --git a/.svelte-kit/env.d.ts b/.svelte-kit/env.d.ts
new file mode 100644
index 0000000..d7f6c97
--- /dev/null
+++ b/.svelte-kit/env.d.ts
@@ -0,0 +1 @@
+// See https://svelte.dev/docs/kit/environment-variables for more information
\ No newline at end of file
diff --git a/.svelte-kit/generated/client/app.js b/.svelte-kit/generated/client/app.js
new file mode 100644
index 0000000..ceb58ac
--- /dev/null
+++ b/.svelte-kit/generated/client/app.js
@@ -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);
\ No newline at end of file
diff --git a/.svelte-kit/generated/client/matchers.js b/.svelte-kit/generated/client/matchers.js
new file mode 100644
index 0000000..f6bd30a
--- /dev/null
+++ b/.svelte-kit/generated/client/matchers.js
@@ -0,0 +1 @@
+export const matchers = {};
\ No newline at end of file
diff --git a/.svelte-kit/generated/client/nodes/0.js b/.svelte-kit/generated/client/nodes/0.js
new file mode 100644
index 0000000..b7f02ca
--- /dev/null
+++ b/.svelte-kit/generated/client/nodes/0.js
@@ -0,0 +1 @@
+export { default as component } from "../../../../web/node_modules/@sveltejs/kit/src/runtime/components/svelte-5/layout.svelte";
\ No newline at end of file
diff --git a/.svelte-kit/generated/client/nodes/1.js b/.svelte-kit/generated/client/nodes/1.js
new file mode 100644
index 0000000..f7e09e9
--- /dev/null
+++ b/.svelte-kit/generated/client/nodes/1.js
@@ -0,0 +1 @@
+export { default as component } from "../../../../web/node_modules/@sveltejs/kit/src/runtime/components/svelte-5/error.svelte";
\ No newline at end of file
diff --git a/.svelte-kit/generated/shared/error-template.js b/.svelte-kit/generated/shared/error-template.js
new file mode 100644
index 0000000..f66e595
--- /dev/null
+++ b/.svelte-kit/generated/shared/error-template.js
@@ -0,0 +1 @@
+export default ({ status, message }) => "\n\n\t
\n\t\t\n\t\t" + message + "\n\n\t\t\n\t\n\t\n\t\t\n\t\t\t
" + status + "\n\t\t\t
\n\t\t\t\t
" + message + "
\n\t\t\t\n\t\t
\n\t\n\n";
\ No newline at end of file
diff --git a/.svelte-kit/tsconfig.json b/.svelte-kit/tsconfig.json
new file mode 100644
index 0000000..f727b03
--- /dev/null
+++ b/.svelte-kit/tsconfig.json
@@ -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"
+ ]
+}
\ No newline at end of file
diff --git a/api/app/services/events.py b/api/app/services/events.py
index f56252d..de2faac 100644
--- a/api/app/services/events.py
+++ b/api/app/services/events.py
@@ -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()
diff --git a/api/tests/test_annotate.py b/api/tests/test_annotate.py
index 811edd0..0ca2ac2 100644
--- a/api/tests/test_annotate.py
+++ b/api/tests/test_annotate.py
@@ -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:p@host.docker.internal: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
diff --git a/web/src/app.css b/web/src/app.css
index d0b82e5..070f438 100644
--- a/web/src/app.css
+++ b/web/src/app.css
@@ -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); } }
diff --git a/web/src/lib/progress.test.ts b/web/src/lib/progress.test.ts
new file mode 100644
index 0000000..97ae8e8
--- /dev/null
+++ b/web/src/lib/progress.test.ts
@@ -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);
+ });
+});
diff --git a/web/src/lib/progress.ts b/web/src/lib/progress.ts
new file mode 100644
index 0000000..659790b
--- /dev/null
+++ b/web/src/lib/progress.ts
@@ -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);
+}
diff --git a/web/src/routes/samples/[id]/+page.svelte b/web/src/routes/samples/[id]/+page.svelte
index 7402699..c3e3b9c 100644
--- a/web/src/routes/samples/[id]/+page.svelte
+++ b/web/src/routes/samples/[id]/+page.svelte
@@ -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(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}
Job {job.id.slice(0, 8)}: {job.status}
+ {#if running}
+
+
+ Annotating for {formatElapsed(elapsedMs)}{#if step} · {step}{/if}
+
+ {/if}
{#if job.status === 'failed' && job.log}
{job.log}
{/if}