diff --git a/.env.default b/.env.default index c5e362ec6..ee5293567 100644 --- a/.env.default +++ b/.env.default @@ -18,12 +18,18 @@ COMPOSE_PROFILES=gpu #GIRDER_ADMIN_USER=admin #GIRDER_ADMIN_PASS=letmein -# Celery connection information +# Girder Worker / Celery (Girder 5 — replaces CELERY_BROKER_URL and WORKER_API_URL) # #RABBITMQ_DEFAULT_USER=guest #RABBITMQ_DEFAULT_PASS=guest #RABBITMQ_DEFAULT_VHOST=default -#CELERY_BROKER_URL=amqp://guest:guest@rabbit/default +#GIRDER_WORKER_BROKER=amqp://guest:guest@rabbit/default +#GIRDER_WORKER_BACKEND=rpc://guest:guest@localhost/ +#GIRDER_SETTING_WORKER_API_URL=http://girder:8080/api/v1 +#GIRDER_NOTIFICATION_REDIS_URL=redis://redis:6379 + +# Docker image tag for kitware/viame-web and workers (Girder 5 builds) +#TAG=girder-5 # RabbitMQ User Queue configs # the user requires administrator permissions in rabbitmq management plugin @@ -60,6 +66,7 @@ COMPOSE_PROFILES=gpu #ACME_EMAIL=changeme@domain.com #ACME_CA_SERVER=https://acme-v02.api.letsencrypt.org/directory #LOG_LEVEL=ERROR -#WORKER_API_URL=https://viame.kitware.com/api/v1 +# Split or standalone worker: remote Girder API (replaces legacy WORKER_API_URL) +#GIRDER_SETTING_WORKER_API_URL=https://viame.kitware.com/api/v1 #SOCK_PATH=/var/run/docker.sock WATCHTOWER_API_TOKEN="customtokenstring" diff --git a/.gitignore b/.gitignore index ed8c57d0c..56f3a90a1 100644 --- a/.gitignore +++ b/.gitignore @@ -108,3 +108,6 @@ venv.bak/ # Notebooks notebooks + +# Synced at runtime in development containers +server/dive_server/dive_client/ diff --git a/README.md b/README.md index a7bfcb921..c1cb22032 100644 --- a/README.md +++ b/README.md @@ -21,10 +21,11 @@ DIVE is a web interface for performing data management, video annotation, and ru * [Server Development Docs](server/README.md) * [Deployment Overview](https://kitware.github.io/dive/Deployment-Overview/) * [Running with Docker Compose](https://kitware.github.io/dive/Deployment-Docker-Compose/) +* [Upgrading to Girder 5](https://kitware.github.io/dive/Deployment-Girder-5-Upgrade/) ## Technologies Used -DIVE uses [Girder](https://girder.readthedocs.io/en/stable/) for data management and has a typical girder + girder worker + docker architecture. See docker scripts for additional details. +DIVE uses [Girder](https://girder.readthedocs.io/en/stable/) 5 for data management and has a typical Girder + Girder Worker + Docker architecture (MongoDB, RabbitMQ, and Redis). See [Running with Docker Compose](https://kitware.github.io/dive/Deployment-Docker-Compose/) and [Upgrading to Girder 5](https://kitware.github.io/dive/Deployment-Girder-5-Upgrade/) for deployment details. * The client application is a standard [@vue/cli](https://cli.vuejs.org/) application. * The job runner is built on celery and [Girder Worker](https://girder-worker.readthedocs.io/en/latest/). Command-line executables for VIAME and FFmpeg are built inside the worker docker image. diff --git a/client/.env.production b/client/.env.production index 9c6b6a99e..fafbee388 100644 --- a/client/.env.production +++ b/client/.env.production @@ -1,4 +1,4 @@ -VUE_APP_STATIC_PATH=./static/viame/ +VUE_APP_STATIC_PATH=/ VUE_APP_GTAG=UA-6042509-43 VUE_APP_SENTRY_DSN=https://0ec02775cc734df98134cecf5c91f782@o267860.ingest.sentry.io/5436001 VUE_APP_UPLOAD_CHUNK_SIZE=67108864 diff --git a/client/electron.vite.config.ts b/client/electron.vite.config.ts index a7e1871bd..04d2dfb52 100644 --- a/client/electron.vite.config.ts +++ b/client/electron.vite.config.ts @@ -94,6 +94,11 @@ export default defineConfig(({ mode }) => { secure: false, ws: true, }, + '/notifications': { + target: apiProxyTarget, + secure: false, + ws: true, + }, }, }, optimizeDeps: { diff --git a/client/package.json b/client/package.json index 93d9193b4..6694a24be 100644 --- a/client/package.json +++ b/client/package.json @@ -31,7 +31,7 @@ }, "dependencies": { "@flatten-js/interval-tree": "^1.0.11", - "@girder/components": "^3.2.0", + "@girder/components": "girder/girder_web_components#girder-5-websocket-upgrade", "@mdi/font": "^6.2.95", "@sentry/browser": "^5.24.2", "@sentry/integrations": "^5.24.2", diff --git a/client/platform/web-girder/plugins/girder.ts b/client/platform/web-girder/plugins/girder.ts index 4853d4273..b6212af98 100644 --- a/client/platform/web-girder/plugins/girder.ts +++ b/client/platform/web-girder/plugins/girder.ts @@ -2,8 +2,10 @@ import Vue from 'vue'; import Girder, { RestClient } from '@girder/components/src'; Vue.use(Girder); +// Attempt to get the token from the cookies or from the localStorage +const localToken = window.localStorage.getItem('girderToken'); const girderRest = new RestClient({ apiRoot: 'api/v1' }); - +girderRest.token = localToken || null; export function useGirderRest() { return girderRest; } diff --git a/client/platform/web-girder/views/Jobs.vue b/client/platform/web-girder/views/Jobs.vue index 80db96855..20c76922d 100644 --- a/client/platform/web-girder/views/Jobs.vue +++ b/client/platform/web-girder/views/Jobs.vue @@ -206,9 +206,11 @@ export default defineComponent({ --gpus all \ --ipc host \ --volume "/opt/noaa/viame:/tmp/addons/extracted:ro" \ + -e "WORKER_CONCURRENCY=2" \ -e "DIVE_USERNAME=username" \ -e "DIVE_PASSWORD=CHANGEME" \ - kitware/viame-worker:latest + -e "DIVE_API_URL=https://viame.kitware.com/api/v1" \ + kitware/viame-worker:girder-5 diff --git a/client/platform/web-girder/views/Login.vue b/client/platform/web-girder/views/Login.vue index 3ea5ac7ef..f028c53c4 100644 --- a/client/platform/web-girder/views/Login.vue +++ b/client/platform/web-girder/views/Login.vue @@ -22,6 +22,9 @@ export default defineComponent({ const { brandData } = useBrand(); const girderRest = useGirderRest(); function onLogin() { + if (girderRest.token) { + window.localStorage.setItem('girderToken', girderRest.token); + } router.push('/'); } girderRest.$on('login', onLogin); diff --git a/client/src/notificatonBus.ts b/client/src/notificatonBus.ts index 0e3acceb6..faa53216c 100644 --- a/client/src/notificatonBus.ts +++ b/client/src/notificatonBus.ts @@ -16,30 +16,22 @@ export interface GirderNotification { /** * Based on Girder Web Components NotificationBus, but simpler. * Register notifications directly on the girderRest instance using - * the EventSource api. + * the WebSocket api. * * @param rc Girder RestClient */ // eslint-disable-next-line @typescript-eslint/no-explicit-any export default function registerNotifications(_rc: any) { const rc: AugmentedRestClient = _rc; // TODO remove after types fixed - const ES = window.EventSource; - const withCredentials = true; - const timeoutSeconds = 300; const retryMsDefault = 8_000; - let since = new Date(); - let lastConnectionAttempt = new Date(); - let eventSourceInstance: EventSource | null = null; + let webSocketInstance: WebSocket | null = null; function connected() { - return !!eventSourceInstance; + return !!webSocketInstance && webSocketInstance.readyState === WebSocket.OPEN; } function emitNotification(notification: GirderNotification) { - const { type, updated } = notification; - if (updated) { - since = new Date(Math.max(+since, +new Date(updated))); - } + const { type } = notification; for (let i = type.indexOf('.'); i !== -1; i = type.indexOf('.', i + 1)) { rc.$emit(`message:${type.substring(0, i)}`, notification); } @@ -47,28 +39,29 @@ export default function registerNotifications(_rc: any) { rc.$emit('message', notification); } - function onSseMessage(e: MessageEvent) { + function onWebSocketMessage(e: MessageEvent) { emitNotification(JSON.parse(e.data)); } function disconnect() { - if (eventSourceInstance) { - eventSourceInstance.close(); + if (webSocketInstance) { + webSocketInstance.close(); } - eventSourceInstance = null; + webSocketInstance = null; } - function onSseError() { - const nowSeconds = Math.ceil(Date.now() / 1000); - const lastSeconds = Math.ceil(+lastConnectionAttempt / 1000); - let retryMs = retryMsDefault; - /** If time since last success is at least half the timeout, it's probably just a timeout */ - if ((nowSeconds - lastSeconds) > (timeoutSeconds * 0.5)) { - retryMs = 0; - } + function onWebSocketError() { disconnect(); // eslint-disable-next-line @typescript-eslint/no-use-before-define - window.setTimeout(connect, retryMs); + window.setTimeout(connect, retryMsDefault); + } + + function onWebSocketClose() { + webSocketInstance = null; + // Attempt to reconnect after a delay + if (rc.user) { + window.setTimeout(connect, retryMsDefault); + } } function connect() { @@ -78,12 +71,20 @@ export default function registerNotifications(_rc: any) { if (!rc.user) { return; } - lastConnectionAttempt = new Date(); - const sinceSeconds = Math.ceil(+since / 1000); - const url = `${rc.apiRoot}/notification/stream?since=${sinceSeconds}&timeout=${timeoutSeconds}`; - eventSourceInstance = new ES(url, { withCredentials }); - eventSourceInstance.onmessage = onSseMessage; - eventSourceInstance.onerror = onSseError; + // Get the token from RestClient + // eslint-disable-next-line @typescript-eslint/no-explicit-any + const { token } = rc as any; + if (!token) { + return; + } + // Construct WebSocket URL from current location + const { protocol, host } = window.location; + const wsProtocol = protocol === 'https:' ? 'wss:' : 'ws:'; + const url = `${wsProtocol}//${host}/notifications/me?token=${token}`; + webSocketInstance = new WebSocket(url); + webSocketInstance.onmessage = onWebSocketMessage; + webSocketInstance.onerror = onWebSocketError; + webSocketInstance.onclose = onWebSocketClose; } rc.$on('login', connect); diff --git a/client/vite.config.ts b/client/vite.config.ts index 28921bc2d..fb568540e 100644 --- a/client/vite.config.ts +++ b/client/vite.config.ts @@ -64,6 +64,12 @@ export default defineConfig(({ mode }) => { secure: false, ws: true, }, + // WebSocket for Girder notifications (not under /api; see notificatonBus.ts). + '/notifications': { + target: apiProxyTarget, + secure: false, + ws: true, + }, }, }, optimizeDeps: { @@ -80,7 +86,7 @@ export default defineConfig(({ mode }) => { }, }, }, - base: mode === 'production' ? '/static/viame/' : '/', + base: '/', test: { globals: true, }, diff --git a/docker-compose.override.yml b/docker-compose.override.yml index 2754a5ef9..f1afcb61c 100644 --- a/docker-compose.override.yml +++ b/docker-compose.override.yml @@ -5,7 +5,9 @@ services: volumes: - ./server:/opt/dive/src - ./docker/server_setup.py:/server_setup.py - command: ["--dev"] + command: ["--mode", "development"] + environment: + - DEVELOPMENT_MODE=True girder_worker_pipelines: volumes: @@ -18,3 +20,7 @@ services: girder_worker_default: volumes: - ./server:/opt/dive/src + + localworker: + volumes: + - ./server:/opt/dive/src diff --git a/docker-compose.yml b/docker-compose.yml index 96b2bdc09..dab3a9035 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -6,7 +6,7 @@ x-worker: &base-worker build: context: . dockerfile: docker/girder_worker.Dockerfile - image: kitware/viame-worker:cpu + image: dive/viame-worker:girder-5-cpu volumes: - addons:/tmp/addons:ro # readonly labels: @@ -34,7 +34,7 @@ services: - "8010:80" rabbit: - image: rabbitmq:3.8.14-management + image: rabbitmq:4.2-management ports: - "5672:5672" - "15672:15672" @@ -49,6 +49,31 @@ services: volumes: # Use env config path, default to docker volume - ${MONGO_DB_PATH:-mongo_db}:/data/db + redis: + image: redis:latest + ports: + - "6379:6379" + volumes: + - redis_data:/data + + localworker: + build: + context: . + dockerfile: docker/girder.Dockerfile + image: kitware/viame-web:${TAG:-girder-5} + profiles: + - gpu + - cpu + depends_on: + - mongo + entrypoint: celery -A girder_worker.app worker -Q local + environment: + - "GIRDER_WORKER_BROKER=${GIRDER_WORKER_BROKER:-amqp://guest:guest@rabbit/default}" + - "GIRDER_WORKER_BACKEND=${GIRDER_WORKER_BACKEND:-rpc://guest:guest@localhost/}" + - "GIRDER_MONGO_URI=mongodb://mongo:27017/girder" + - "GIRDER_NOTIFICATION_REDIS_URL=redis://redis:6379" + - "C_FORCE_ROOT=1" + # Memcache is used for caching girder-large-images, should auto configure with it being present memcached: image: memcached @@ -58,7 +83,7 @@ services: build: context: . dockerfile: docker/girder.Dockerfile - image: kitware/viame-web:${TAG:-latest} + image: kitware/viame-web:${TAG:-girder-5} init: true command: ["--mode", "production"] depends_on: @@ -76,8 +101,12 @@ services: - "GIRDER_MONGO_URI=mongodb://mongo:27017/girder" - "GIRDER_ADMIN_USER=${GIRDER_ADMIN_USER:-admin}" - "GIRDER_ADMIN_PASS=${GIRDER_ADMIN_PASS:-letmein}" - - "CELERY_BROKER_URL=${CELERY_BROKER_URL:-amqp://guest:guest@rabbit/default}" - - "WORKER_API_URL=${WORKER_API_URL:-http://girder:8080/api/v1}" + - "GIRDER_WORKER_BROKER=${GIRDER_WORKER_BROKER:-amqp://guest:guest@rabbit/default}" + - "GIRDER_WORKER_BACKEND=${GIRDER_WORKER_BACKEND:-rpc://guest:guest@localhost/}" + - "GIRDER_SETTING_WORKER_API_URL=${GIRDER_SETTING_WORKER_API_URL:-http://girder:8080/api/v1}" + - "GIRDER_STATIC_ROOT_DIR=/opt/dive/clients/girder" + - "GIRDER_NOTIFICATION_REDIS_URL=redis://redis:6379" + # Rabbitmq management variables - "RABBITMQ_MANAGEMENT_USERNAME=${RABBITMQ_MANAGEMENT_USERNAME:-guest}" - "RABBITMQ_MANAGEMENT_PASSWORD=${RABBITMQ_MANAGEMENT_PASSWORD:-guest}" @@ -109,7 +138,9 @@ services: environment: - "WORKER_WATCHING_QUEUES=celery" - "WORKER_CONCURRENCY=${DEFAULT_WORKER_CONCURRENCY:-3}" - - "CELERY_BROKER_URL=${CELERY_BROKER_URL:-amqp://guest:guest@rabbit/default}" + - "GIRDER_WORKER_BROKER=${GIRDER_WORKER_BROKER:-amqp://guest:guest@rabbit/default}" + - "GIRDER_WORKER_BACKEND=${GIRDER_WORKER_BACKEND:-rpc://guest:guest@localhost/}" + - "GIRDER_SETTING_WORKER_API_URL=${GIRDER_SETTING_WORKER_API_URL:-http://girder:8080/api/v1}" girder_worker_pipelines: # Merge base-worker object with this config @@ -121,7 +152,7 @@ services: build: context: . dockerfile: docker/girder_worker_gpu.Dockerfile - image: kitware/viame-worker:gpu + image: dev/viame-worker:girder-5gpu restart: always deploy: resources: @@ -135,7 +166,12 @@ services: - "WORKER_WATCHING_QUEUES=pipelines" - "WORKER_CONCURRENCY=${PIPELINE_WORKER_CONCURRENCY:-1}" - "WORKER_GPU_UUID=${PIPELINE_GPU_UUID}" + - "GIRDER_WORKER_BROKER=${GIRDER_WORKER_BROKER:-amqp://guest:guest@rabbit/default}" - "CELERY_BROKER_URL=${CELERY_BROKER_URL:-amqp://guest:guest@rabbit/default}" + - "GIRDER_WORKER_BACKEND=${GIRDER_WORKER_BACKEND:-rpc://guest:guest@localhost/}" + - "GIRDER_SETTING_WORKER_API_URL=${GIRDER_SETTING_WORKER_API_URL:-http://girder:8080/api/v1}" + - "GIRDER_MONGO_URI=mongodb://mongo:27017/girder" + - "GIRDER_NOTIFICATION_REDIS_URL=redis://redis:6379" healthcheck: test: ["CMD", "nvidia-smi"] interval: 15m @@ -166,7 +202,10 @@ services: - "WORKER_WATCHING_QUEUES=training" - "WORKER_CONCURRENCY=${TRAINING_WORKER_CONCURRENCY:-1}" - "WORKER_GPU_UUID=${TRAINING_GPU_UUID}" + - "GIRDER_WORKER_BROKER=${GIRDER_WORKER_BROKER:-amqp://guest:guest@rabbit/default}" - "CELERY_BROKER_URL=${CELERY_BROKER_URL:-amqp://guest:guest@rabbit/default}" + - "GIRDER_WORKER_BACKEND=${GIRDER_WORKER_BACKEND:-rpc://guest:guest@localhost/}" + - "GIRDER_SETTING_WORKER_API_URL=${GIRDER_SETTING_WORKER_API_URL:-http://girder:8080/api/v1}" healthcheck: test: ["CMD", "nvidia-smi"] interval: 15m @@ -193,3 +232,4 @@ volumes: addons: mongo_db: girder_assetstore: + redis_data: diff --git a/docker/entrypoint_server.sh b/docker/entrypoint_server.sh index 42d4429f4..d5083d43b 100755 --- a/docker/entrypoint_server.sh +++ b/docker/entrypoint_server.sh @@ -1,9 +1,22 @@ #!/bin/sh + +if [ "$DEVELOPMENT_MODE" = "True" ]; then + echo "Development mode is enabled, syncing client builds..." + echo "Syncing Dive client..." + cp -r /opt/dive/clients/dive/ /opt/dive/src/dive_server/dive_client/ +fi + set -e # Ensure reload/watch paths stay in project source, not filesystem root. cd /opt/dive/src +# Remove stale project virtualenvs from mounted source trees. +# Runtime uses /opt/dive/local/venv; stale .venv paths can crash uvicorn reload scanning. +if [ -e /opt/dive/src/.venv ] || [ -L /opt/dive/src/.venv ]; then + rm -rf /opt/dive/src/.venv +fi + # Backward compatibility for older compose overrides. if [ "$1" = "--dev" ]; then shift diff --git a/docker/entrypoint_worker.sh b/docker/entrypoint_worker.sh index 717c0d603..decf9d1fc 100755 --- a/docker/entrypoint_worker.sh +++ b/docker/entrypoint_worker.sh @@ -9,7 +9,7 @@ QUEUE_ARGUMENT= CONCURRENCY_ARGUMENT= if [ -n "$WORKER_WATCHING_QUEUES" ]; then - QUEUE_ARGUMENT="--queues $WORKER_WATCHING_QUEUES" + QUEUE_ARGUMENT="-Q $WORKER_WATCHING_QUEUES" fi if [ -n "$WORKER_CONCURRENCY" ]; then diff --git a/docker/girder.Dockerfile b/docker/girder.Dockerfile index 98ad0d9dc..0e1a52f62 100644 --- a/docker/girder.Dockerfile +++ b/docker/girder.Dockerfile @@ -12,6 +12,16 @@ COPY .git/ /app/.git/ COPY client/ /app/ RUN npm run build:web +FROM node:24.15.0 AS girder-client-builder +WORKDIR /app +RUN apt-get update && apt-get install -y git +# make sure I clone +ARG CACHEBUST=2 +RUN git clone https://github.com/girder/girder.git +RUN cd girder/girder && cd web && npm install --include=optional && npx vite build --base=/girder/ + + + # ======================== # == SERVER BUILD STAGE == # ======================== @@ -22,10 +32,13 @@ SHELL ["/bin/bash", "-c"] WORKDIR /opt/dive/src RUN apt-get update && \ apt-get install -y --no-install-recommends \ - curl && \ + curl git && \ apt-get clean && \ rm -rf /var/lib/apt/lists/* +# https://cryptography.io/en/latest/installation/#debian-ubuntu +RUN apt-get update +RUN apt-get install -y build-essential libssl-dev libffi-dev python3-libtiff libgdal-dev python3-dev cargo nodejs npm ENV UV_COMPILE_BYTECODE=1 UV_LINK_MODE=copy ENV VIRTUAL_ENV="/opt/dive/local/venv" ENV UV_PROJECT_ENVIRONMENT=/opt/dive/local/venv @@ -35,22 +48,9 @@ RUN uv venv /opt/dive/local/venv # Copy only the lock and project files to optimize cache COPY server/pyproject.toml server/uv.lock /opt/dive/src/ RUN uv sync --frozen --no-install-project --no-dev --extra large-image -# Install Node.js (kept for any plugin/frontend build tooling invoked by deps) -RUN curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.5/install.sh | bash - -# Default node version -RUN . ~/.bashrc && \ - nvm install 14 && \ - nvm alias default 14 && \ - nvm use default && \ - ln -s $(dirname `which npm`) /usr/local/node - -ENV PATH="/usr/local/node:$PATH" - # Copy full source code and install COPY server/ /opt/dive/src/ RUN uv sync --frozen --no-dev --extra large-image -RUN uv run girder build # ================= # == DIST SERVER == @@ -68,10 +68,9 @@ COPY --from=server-builder /opt/dive/local/venv /opt/dive/local/venv # Copy the source code of the editable module COPY --from=server-builder /opt/dive/src /opt/dive/src # Copy the client code into the static source location -COPY --from=client-builder /app/dist/ /opt/dive/local/venv/share/girder/static/viame/ -# Copy uv binary for runtime use -COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv +COPY --from=client-builder /app/dist/ /opt/dive/clients/dive +COPY --from=girder-client-builder /app/girder/girder/web/dist/ /opt/dive/clients/girder # Install startup scripts COPY docker/entrypoint_server.sh docker/server_setup.py / - +RUN export GIRDER_STATIC_ROOT_DIR=/opt/dive/clients/girder ENTRYPOINT [ "/entrypoint_server.sh" ] diff --git a/docker/girder_worker.Dockerfile b/docker/girder_worker.Dockerfile index 35c4fc725..2e56b0468 100644 --- a/docker/girder_worker.Dockerfile +++ b/docker/girder_worker.Dockerfile @@ -2,7 +2,7 @@ FROM python:3.11-bookworm AS worker # install architecture-compatible tini and ffmpeg RUN apt-get update && \ - apt-get install -qy tini ffmpeg && \ + apt-get install -qy tini ffmpeg git && \ apt-get clean && rm -rf /var/lib/apt/lists/* # use distro-provided tini binary for current architecture @@ -24,8 +24,6 @@ ENV PATH="/opt/dive/local/venv/bin:/usr/local/bin:$PATH" COPY server/pyproject.toml server/uv.lock /opt/dive/src/ # Install dependencies only RUN uv sync --frozen --no-install-project --no-dev -# Build girder client, including plugins like worker/jobs -# RUN girder build # Copy full source code and install COPY server/ /opt/dive/src/ diff --git a/docker/server_setup.py b/docker/server_setup.py index a0e38edb6..105e9dc68 100644 --- a/docker/server_setup.py +++ b/docker/server_setup.py @@ -10,8 +10,6 @@ from girder.models.user import User from pymongo.errors import OperationFailure -cherrypy.config["database"]["uri"] = os.getenv("GIRDER_MONGO_URI") - ADMIN_USER = os.getenv("GIRDER_ADMIN_USER", "admin") ADMIN_PASS = os.getenv("GIRDER_ADMIN_PASS", "letmein") diff --git a/docs/Deployment-Docker-Compose.md b/docs/Deployment-Docker-Compose.md index e10764f2a..67f9d5270 100644 --- a/docs/Deployment-Docker-Compose.md +++ b/docs/Deployment-Docker-Compose.md @@ -8,12 +8,18 @@ Start here once you have SSH access and `sudo` privileges for a server or VM. ## Container Images -A DIVE Web deployment consists of 2 main services. +A DIVE Web deployment consists of 2 main application images (Girder 5 builds use the `girder-5` tag unless overridden with `TAG` in `.env`): -* [kitware/viame-web](https://hub.docker.com/r/kitware/viame-web) - the web server -* [kitware/viame-worker](https://hub.docker.com/r/kitware/viame-worker) - the queue worker +* [kitware/viame-web](https://hub.docker.com/r/kitware/viame-web) — Girder web server and bundled Vue client +* [kitware/viame-worker](https://hub.docker.com/r/kitware/viame-worker) — Celery workers for transcoding, pipelines, and training -In addition, a database (MongoDB) and a queue service (RabbitMQ) are required. +Infrastructure services required by the stack: + +* **MongoDB** — Girder database +* **RabbitMQ** — Celery message broker +* **Redis** — Girder notification fan-out (job status and UI updates over WebSockets) + +Upgrading from Girder 3? See [Upgrading to Girder 5](Deployment-Girder-5-Upgrade.md). ![DIVE-Web-Architecture-Diagram.svg](images/Diagrams/DIVE-Web-Architecture-Diagram.svg) @@ -106,11 +112,15 @@ It's possible to split your web server and task runner between multiple nodes. * Make two cloud VM instances, one with NVIDIA drivers and container toolkit, and one without. This is still a special case of scenario 1 from the [Provisioning Guide](Deployment-Provision.md) * Clone the dive repository on both, and set up `.env` on both with the same configuration. -* Be sure that `WORKER_API_URL` and `CELERY_BROKER_URL` in particular are uncommented and set to the IP or domain name of your web server. This is how the worker will talk to the web server, so the web server must be network accessible from the worker. +* On worker nodes, uncomment and set: + * `GIRDER_WORKER_BROKER` — RabbitMQ URL reachable on the web server (e.g. `amqp://guest:guest@your-web-host/default`) + * `GIRDER_SETTING_WORKER_API_URL` — Girder API URL on the web server (e.g. `http://your-web-host:8080/api/v1`) + * `GIRDER_NOTIFICATION_REDIS_URL` — Redis URL on the web server if workers use the same notification settings as Compose (e.g. `redis://your-web-host:6379`) +* The web server must be network-accessible from workers for the API URL and from workers to RabbitMQ and Redis. ``` bash ## On the web server -docker-compose -f docker-compose.yml up -d girder rabbit +docker-compose -f docker-compose.yml up -d girder rabbit mongo redis ## On the GPU server(s) docker-compose -f docker-compose.yml up -d --no-deps girder_worker_default girder_worker_pipelines girder_worker_training @@ -172,8 +182,11 @@ This image contains both the backend and client. | GIRDER_MONGO_URI | `mongodb://mongo:27017/girder` | a mongodb connection string | | GIRDER_ADMIN_USER | `admin` | admin username | | GIRDER_ADMIN_PASS | `letmein` | admin password | -| CELERY_BROKER_URL | `amqp://guest:guest@default/` | rabbitmq connection string | -| WORKER_API_URL | `http://girder:8080/api/v1` | Address for workers to reach web server | +| GIRDER_WORKER_BROKER | `amqp://guest:guest@rabbit/default` | RabbitMQ connection string (Celery broker) | +| GIRDER_WORKER_BACKEND | `rpc://guest:guest@localhost/` | Celery result backend (RPC) | +| GIRDER_SETTING_WORKER_API_URL | `http://girder:8080/api/v1` | Girder REST API URL used by workers | +| GIRDER_NOTIFICATION_REDIS_URL | `redis://redis:6379` | Redis URL for notification fan-out | +| GIRDER_STATIC_ROOT_DIR | `/opt/dive/clients/girder` | Built web client static files (set in image/Compose) | There is additional configuration for the RabbitMQ Management plugin. It only matters if you intend to allow individual users to configure private job runners in standalone mode, and can otherwise be ignored. @@ -181,7 +194,7 @@ There is additional configuration for the RabbitMQ Management plugin. It only ma |----------|---------|-------------| | RABBITMQ_MANAGEMENT_USERNAME | `guest` | Management API username | | RABBITMQ_MANAGEMENT_PASSWORD | `guest` | Management API password | -| RABBITMQ_MANAGEMENT_VHOST | `default` | Virtual host should match `CELERY_BROKER_URL` | +| RABBITMQ_MANAGEMENT_VHOST | `default` | Virtual host should match `GIRDER_WORKER_BROKER` | | RABBITMQ_MANAGEMENT_URL | `http://rabbit:15672/` | Management API Url | You can also pass [girder configuration](https://girder.readthedocs.io/en/latest/) and [celery configuration](https://docs.celeryproject.org/en/stable/userguide/configuration.html#std-setting-broker_connection_timeout). @@ -197,7 +210,9 @@ This image contains a celery worker to run VIAME pipelines and transcoding jobs. | WORKER_WATCHING_QUEUES | null | one of `celery`, `pipelines`, `training`. Ignored in standalone mode. | | WORKER_CONCURRENCY | `# of CPU cores` | max concurrnet jobs. **Lower this if you run training** | | WORKER_GPU_UUID | null | leave empty to use all GPUs. Specify UUID to use specific device | -| CELERY_BROKER_URL | `amqp://guest:guest@default/` | rabbitmq connection string. Ignored in standalone mode. | +| GIRDER_WORKER_BROKER | `amqp://guest:guest@rabbit/default` | RabbitMQ connection string. Ignored in standalone mode. | +| GIRDER_SETTING_WORKER_API_URL | `http://girder:8080/api/v1` | Girder API URL (split/multi-node deployments). Ignored in standalone mode when using `DIVE_API_URL`. | +| GIRDER_NOTIFICATION_REDIS_URL | `redis://redis:6379` | Redis for notifications when running workers in Compose | | KWIVER_DEFAULT_LOG_LEVEL | `warn` | Log level for VIAME pipeline jobs (env name unchanged; used by the Kwiver logging stack) | | DIVE_USERNAME | null | Username to start private queue processor. Providing this enables standalone mode. | | DIVE_PASSWORD | null | Password for private queue processor. Providing this enables standalone mode. | @@ -228,5 +243,9 @@ docker run --rm --name dive_worker \ -e "DIVE_USERNAME=CHANGEME" \ -e "DIVE_PASSWORD=CHANGEME" \ -e "DIVE_API_URL=https://viame.kitware.com/api/v1" \ - kitware/viame-worker:latest + kitware/viame-worker:girder-5 ``` + +### Development: `localworker` + +With `docker-compose.override.yml`, Compose also starts a **`localworker`** service that runs `celery -A girder_worker.app worker -Q local` for development tasks. It is not required for production; see [Upgrading to Girder 5](Deployment-Girder-5-Upgrade.md). diff --git a/docs/Deployment-Girder-5-Upgrade.md b/docs/Deployment-Girder-5-Upgrade.md new file mode 100644 index 000000000..3a98150ca --- /dev/null +++ b/docs/Deployment-Girder-5-Upgrade.md @@ -0,0 +1,58 @@ +# Upgrading to Girder 5 + +Current DIVE Web releases run on **Girder 5** with updated worker plugins, notification delivery, and Docker Compose configuration. Use this page when upgrading an existing Girder 3 deployment or aligning a custom `.env` with the current stack. + +For general deployment steps, see [Running with Docker Compose](Deployment-Docker-Compose.md). For upstream Girder API and plugin changes, see the [Girder migration guide](https://github.com/girder/girder/blob/v4-integration/docs/migration-guide.rst). + +## Summary of infrastructure changes + +| Change | Action required | +|--------|-----------------| +| **Girder 5** | Pull or build images tagged `girder-5` (see `TAG` in `.env`). | +| **Redis** | Add a Redis service; required for job and UI notifications. | +| **Notifications** | The web client uses WebSockets (not the legacy Girder EventStream). Ensure browsers can reach the Girder API and that Redis is running. | +| **Environment variables** | Rename broker and worker API settings (table below). | +| **Static client** | Girder no longer runs `girder build` in the image; the Vue app is built into the image at `GIRDER_STATIC_ROOT_DIR`. | + +## Environment variable renames + +Update your `.env` (and any external orchestration) to use Girder 5 names: + +| Girder 4 / legacy name | Girder 5 name | Purpose | +|------------------------|---------------|---------| +| `CELERY_BROKER_URL` | `GIRDER_WORKER_BROKER` | RabbitMQ URL for Celery (message broker). | +| `WORKER_API_URL` | `GIRDER_SETTING_WORKER_API_URL` | Girder REST API URL workers call (e.g. `http://girder:8080/api/v1`). | +| *(not used)* | `GIRDER_WORKER_BACKEND` | Celery result backend (Compose default: `rpc://guest:guest@localhost/`). | +| *(not used)* | `GIRDER_NOTIFICATION_REDIS_URL` | Redis URL for Girder notification fan-out (e.g. `redis://redis:6379`). | +| *(not used)* | `GIRDER_STATIC_ROOT_DIR` | Path to built web client inside the Girder container (set in Compose). | + +`GIRDER_WORKER_BACKEND` is **not** a replacement for `WORKER_API_URL`. Do not point it at `http://…/api/v1`; use `GIRDER_SETTING_WORKER_API_URL` for that. + +## Recommended upgrade steps + +1. **Back up** MongoDB and any asset store data before upgrading. +2. **Merge or checkout** the Girder 5 branch and copy `.env.default` changes into your `.env`. +3. **Set image tag**, for example `TAG=girder-5`, or pull images that publish that tag. +4. **Add Redis** — use the `redis` service from `docker-compose.yml` or an external Redis instance and set `GIRDER_NOTIFICATION_REDIS_URL` on `girder` and all worker services. +5. **Rename variables** in `.env` per the table above. +6. **Multi-node deployments:** set `GIRDER_WORKER_BROKER` to your RabbitMQ URL and `GIRDER_SETTING_WORKER_API_URL` to your Girder API URL on every worker host; workers must reach Redis used by the web tier if they rely on notification-related features configured in Compose. +7. **Rebuild or pull** images, then restart the stack: + +```bash +docker-compose -f docker-compose.yml pull +docker-compose -f docker-compose.yml up -d +``` + +8. **Smoke-test** login, job launch, pipeline/training jobs, and job status updates in the UI (confirms WebSocket notifications and Redis). + +## Development-only: `localworker` + +When using `docker-compose.override.yml`, a **`localworker`** service runs Celery on the `local` queue for tasks that should not go through the main worker pool. This service is for local development only and is not required for production deployments. + +## Python dependencies + +Server packages pin Girder 5 (`girder`, `girder_jobs`, `girder_worker`, etc. at 5.0.x in `server/pyproject.toml`). Regenerate the lockfile from `server/` if you change plugin versions: + +```bash +cd server && uv lock +``` diff --git a/docs/Deployment-Overview.md b/docs/Deployment-Overview.md index bad1e8ee0..778af7a94 100644 --- a/docs/Deployment-Overview.md +++ b/docs/Deployment-Overview.md @@ -33,7 +33,7 @@ The easiest option to get started using VIAME is to [try our public server](Web- ## Running your own instance -You may wish to run your own deployment of VIAME Web in your lab or a cloud environment. Deploying VIAME Web is relatively straightforward with `docker-compose`. +You may wish to run your own deployment of VIAME Web in your lab or a cloud environment. Deploying VIAME Web is relatively straightforward with `docker-compose`. If you are upgrading an existing Girder 3 deployment, start with [Upgrading to Girder 5](Deployment-Girder-5-Upgrade.md). By default, Docker Compose starts DIVE with GPU pipeline/training workers enabled. Use `--profile cpu` when launching Compose to run CPU-only workers. diff --git a/mkdocs.yml b/mkdocs.yml index db2a6c0d6..caf464fb0 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -77,6 +77,7 @@ nav: - Deployment Options Overview: Deployment-Overview.md - Provisioning Google Cloud: Deployment-Provision.md - Running with Docker Compose: Deployment-Docker-Compose.md + - Upgrading to Girder 5: Deployment-Girder-5-Upgrade.md - Cloud Storage Integration: Deployment-Storage.md - REST API Specification: https://viame.kitware.com/api/v1 - Scripting: diff --git a/server/README.md b/server/README.md index 6a0cffe84..a058aff5b 100644 --- a/server/README.md +++ b/server/README.md @@ -7,6 +7,14 @@ There are several important python packages in this application * `scripts` has general command-line utilities * `dive_utils` is shared code between the above packages +## Girder 5 stack + +The server targets **Girder 5** (`girder`, `girder_jobs`, `girder_worker`, and related plugins pinned in `pyproject.toml`). Docker Compose adds **Redis** for notifications (`GIRDER_NOTIFICATION_REDIS_URL`); the web client receives job updates over WebSockets. + +When developing with `docker-compose.override.yml`, a **`localworker`** service runs Celery on the `local` queue in addition to the standard workers. + +Upgrading an existing deployment: [Upgrading to Girder 5](https://kitware.github.io/dive/Deployment-Girder-5-Upgrade/). + ## Prerequisites Set up your system as described in the [Basic Deployment](https://kitware.github.io/dive/Deployment-Docker-Compose/) diff --git a/server/bucket_notifications/views.py b/server/bucket_notifications/views.py index 1961be9c9..0e7fa670b 100644 --- a/server/bucket_notifications/views.py +++ b/server/bucket_notifications/views.py @@ -1,7 +1,7 @@ +import logging import os from bson.objectid import ObjectId -from girder import logger from girder.api import access from girder.api.describe import Description, autoDescribeRoute from girder.api.rest import Resource @@ -11,11 +11,14 @@ from girder.models.folder import Folder from girder.models.user import User +from dive_tasks.local_tasks import import_assetstore_path_async from dive_utils.types import AssetstoreModel, GirderModel from .constants import AssetstoreRuleMarker from .models import GCSNotificationRecord, GCSPushNotificationPayload, NotificationRouterRule +logger = logging.getLogger(__name__) + class BucketNotification(Resource): def __init__(self): @@ -71,14 +74,14 @@ def processNotification(store: AssetstoreModel, rootFolder: GirderModel, importP # All the chain of parent directories exist realImportPath = importPath - Assetstore().importData( - store, - target, + import_assetstore_path_async.delay( + str(store['_id']), + str(target['_id']), 'folder', - {'importPath': realImportPath}, - None, - owner, + realImportPath, + str(owner['_id']), force_recursive=False, + leaf_folders_as_items=False, ) @access.admin diff --git a/server/dive_server/__init__.py b/server/dive_server/__init__.py index 37e0dea23..37fa0fc58 100644 --- a/server/dive_server/__init__.py +++ b/server/dive_server/__init__.py @@ -1,4 +1,5 @@ import os +import logging from pathlib import Path from girder import events, plugin @@ -12,15 +13,20 @@ from dive_utils import constants -from .client_webroot import ClientWebroot from .crud_annotation import GroupItem, RevisionLogItem, TrackItem -from .event import DIVES3Imports, process_fs_import, process_s3_import, send_new_user_email +from .event import send_new_user_email from .views_annotation import AnnotationResource from .views_configuration import ConfigurationResource from .views_dataset import DatasetResource -from .views_override import countJobs, use_private_queue, list_shared_folders, get_root_path_or_relative +from .views_override import ( + countJobs, + get_root_path_or_relative, + list_shared_folders, + use_private_queue, +) from .views_rpc import RpcResource +logger = logging.getLogger(__name__) class GirderPlugin(plugin.GirderPlugin): def load(self, info): @@ -38,7 +44,9 @@ def load(self, info): info['apiRoot'].job.route("GET", ("queued",), countJobs) info["apiRoot"].user.route("PUT", (":id", "use_private_queue"), use_private_queue) info["apiRoot"].folder.route("GET", ("shared-folders",), list_shared_folders) - info["apiRoot"].folder.route("GET", (":id", "rootpath_or_relative"), get_root_path_or_relative) + info["apiRoot"].folder.route( + "GET", (":id", "rootpath_or_relative"), get_root_path_or_relative + ) User().exposeFields(AccessType.READ, constants.UserPrivateQueueEnabledMarker) # Expose Job dataset assocation @@ -47,49 +55,22 @@ def load(self, info): DIVE_MAIL_TEMPLATES = Path(os.path.realpath(__file__)).parent / 'mail_templates' mail_utils.addTemplateDirectory(str(DIVE_MAIL_TEMPLATES)) - # Relocate Girder - info["serverRoot"], info["serverRoot"].girder = ( - ClientWebroot(), - info["serverRoot"], - ) - info["serverRoot"].api = info["serverRoot"].girder.api + core_girder = info['serverRoot'].apps[''] + core_girder.script_name = '/girder' + info['serverRoot'].mount(core_girder, '/girder', core_girder.config) + del info['serverRoot'].apps[''] - diveS3Import = DIVES3Imports() - events.bind( - "rest.post.assetstore/:id/import.before", - "process_s3_import_before", - diveS3Import.process_s3_import_before, - ) - events.bind( - "rest.post.assetstore/:id/import.after", - "process_s3_import_after", - diveS3Import.process_s3_import_after, - ) - events.bind( - "filesystem_assetstore_imported", - "process_fs_import", - process_fs_import, - ) - events.bind( - "s3_assetstore_imported", - "process_s3_import", - process_s3_import, - ) + conf = { + '/': { + 'tools.staticdir.on': True, + 'tools.staticdir.dir': '/opt/dive/clients/dive', + 'tools.staticdir.index': 'index.html', + }, + } + info['serverRoot'].mount(None, '', conf) events.bind( 'model.user.save.created', 'send_new_user_email', send_new_user_email, ) - - # Create dependency on worker - plugin.getPlugin('worker').load(info) - Setting().set( - 'worker.api_url', - os.environ.get('WORKER_API_URL', 'http://girder:8080/api/v1'), - ) - - broker_url = os.environ.get('CELERY_BROKER_URL', None) - if broker_url is None: - raise RuntimeError('CELERY_BROKER_URL must be set') - Setting().set('worker.broker', broker_url) diff --git a/server/dive_server/crud_override.py b/server/dive_server/crud_override.py index ce05bbdc3..249d487b9 100644 --- a/server/dive_server/crud_override.py +++ b/server/dive_server/crud_override.py @@ -1,30 +1,43 @@ -import cherrypy - from typing import Tuple -from dive_utils import types - +import cherrypy +from girder.constants import AccessType from girder.models.folder import Folder from girder.models.user import User -from girder.constants import AccessType -def get_folders_shared_with_me_query( - user: types.GirderUserModel, - prefix: str = '' -): +from dive_utils import types + + +def get_folders_shared_with_me_query(user: types.GirderUserModel, prefix: str = ''): return { '$and': [ # Folders expicilty set public are hidden (can also be False or None) {'$nor': [{'public': True}]}, - # Find folders not owned by the current user - {'$nor': [{prefix + 'creatorId': {'$eq': user['_id']}}, {prefix + 'creatorId': {'$eq': None}}]}, - - # But where the current user, or one group it belongs, has been given explicit access + { + '$nor': [ + {prefix + 'creatorId': {'$eq': user['_id']}}, + {prefix + 'creatorId': {'$eq': None}}, + ] + }, + # But where the current user, or one group it belongs, has been given explicit access { '$or': [ - {prefix + 'access.users': {'$elemMatch': {'id': user['_id'], 'level': {'$gte': AccessType.READ}}}}, - {prefix + 'access.groups': {'$elemMatch': {'id': {'$in': user.get('groups', [])}, 'level': {'$gte': AccessType.READ}}}}, + { + prefix + + 'access.users': { + '$elemMatch': {'id': user['_id'], 'level': {'$gte': AccessType.READ}} + } + }, + { + prefix + + 'access.groups': { + '$elemMatch': { + 'id': {'$in': user.get('groups', [])}, + 'level': {'$gte': AccessType.READ}, + } + } + }, ] }, ] @@ -35,39 +48,36 @@ def get_only_root_folders_shared_with_me_pipeline( user: types.GirderUserModel, ): pipeline: list[dict] = [] - pipeline.append({ - '$match': get_folders_shared_with_me_query(user) - }) + pipeline.append({'$match': get_folders_shared_with_me_query(user)}) # Join parent folder to selected ones - pipeline.append({ - '$lookup': { - 'from': 'folder', - 'localField': 'parentId', - 'foreignField': '_id', - 'as': 'parent' + pipeline.append( + { + '$lookup': { + 'from': 'folder', + 'localField': 'parentId', + 'foreignField': '_id', + 'as': 'parent', + } } - }) + ) # Transform parent array as single object - pipeline.append({ - '$unwind': { - 'path': '$parent', - 'preserveNullAndEmptyArrays': True - } - }) + pipeline.append({'$unwind': {'path': '$parent', 'preserveNullAndEmptyArrays': True}}) # Filter folders to show depending on parent - pipeline.append({ - '$match': { - '$or': [ - # Only show folders that have no parent - {'parent': None}, - # Or whose parent is not shared to the user - {'$nor': [get_folders_shared_with_me_query(user, prefix='parent.')]} - ] + pipeline.append( + { + '$match': { + '$or': [ + # Only show folders that have no parent + {'parent': None}, + # Or whose parent is not shared to the user + {'$nor': [get_folders_shared_with_me_query(user, prefix='parent.')]}, + ] + } } - }) + ) return pipeline @@ -77,7 +87,7 @@ def list_shared_folders( limit: int, offset: int, sortParams: Tuple[Tuple[str, int]], - onlyNonAccessibles: bool = True + onlyNonAccessibles: bool = True, ): sort, sortDir = (sortParams or [['created', 1]])[0] if sort == 'type': @@ -86,9 +96,7 @@ def list_shared_folders( if onlyNonAccessibles: pipeline = get_only_root_folders_shared_with_me_pipeline(user) else: - pipeline = [{ - '$match': get_folders_shared_with_me_query(user) - }] + pipeline = [{'$match': get_folders_shared_with_me_query(user)}] # based on https://stackoverflow.com/a/49483919 pipeline += [ @@ -120,13 +128,10 @@ def list_shared_folders( return [Folder().filter(doc, additionalKeys=['ownerLogin']) for doc in response['results']] -def get_root_path_or_relative( - user: types.GirderUserModel, - folder: types.GirderModel -): +def get_root_path_or_relative(user: types.GirderUserModel, folder: types.GirderModel): path_to_folder = Folder().parentsToRoot(folder, force=True, user=user) final_path = [] - + for item in reversed(path_to_folder): if item['type'] == 'folder': if not Folder().hasAccess(item['object'], user, AccessType.READ): @@ -134,10 +139,7 @@ def get_root_path_or_relative( creator = User().findOne({'_id': item['object']['creatorId']}) if creator: creator = User().filter(creator, user) - final_path.append({ - 'type': 'user', - 'object': creator - }) + final_path.append({'type': 'user', 'object': creator}) break item['object'] = Folder().filter(item['object'], user) final_path.append(item) @@ -147,4 +149,4 @@ def get_root_path_or_relative( final_path.append(item) break - return list(reversed(final_path)) \ No newline at end of file + return list(reversed(final_path)) diff --git a/server/dive_server/crud_rpc.py b/server/dive_server/crud_rpc.py index defce5a6d..d65e8e951 100644 --- a/server/dive_server/crud_rpc.py +++ b/server/dive_server/crud_rpc.py @@ -7,11 +7,11 @@ from girder.models.file import File from girder.models.folder import Folder from girder.models.item import Item -from girder.models.notification import Notification from girder.models.setting import Setting from girder.models.token import Token +from girder.notification import Notification from girder_jobs.models.job import Job, JobStatus -from girder_worker.girder_plugin.status import CustomJobStatus +from girder_plugin_worker.status import CustomJobStatus from pydantic import BaseModel import pymongo @@ -65,8 +65,10 @@ def _load_dynamic_pipelines(user: types.GirderUserModel) -> Dict[str, types.Pipe """Add any additional dynamic pipelines to the existing pipeline list.""" pipelines: Dict[str, types.PipelineCategory] = {} pipelines[constants.TrainedPipelineCategory] = {"pipes": [], "description": ""} - - trained_pipelines_query = {f"meta.{constants.TrainedPipelineMarker}": {'$in': TRUTHY_META_VALUES}} + + trained_pipelines_query = { + f"meta.{constants.TrainedPipelineMarker}": {'$in': TRUTHY_META_VALUES} + } query = {'$and': [trained_pipelines_query, Folder().permissionClauses(user, AccessType.READ)]} models = [ {'$match': query}, @@ -124,7 +126,14 @@ def _load_dynamic_models(user: types.GirderUserModel) -> Dict[str, types.Trainin for item in Folder().childItems(folder): is_training_model = False match = None - match = next((extension for extension in TrainingModelExtensions if item['name'].endswith(extension)), None) + match = next( + ( + extension + for extension in TrainingModelExtensions + if item['name'].endswith(extension) + ), + None, + ) if match is not None: is_training_model = True if is_training_model and not item['name'].startswith('embedded_') and match: @@ -256,14 +265,14 @@ def run_pipeline( Job().copyAccessPolicies(folder, newjob.job) Job().save(newjob.job) # Inform Client of new Job added in inactive state - Notification().createNotification( + Notification( type='job_status', data=newjob.job, user=user, - expires=datetime.now() + timedelta(seconds=30), - ) + ).flush() return newjob.job + def export_trained_pipeline( user: types.GirderUserModel, model_folder: types.GirderModel, @@ -300,14 +309,14 @@ def export_trained_pipeline( Job().copyAccessPolicies(model_folder, newjob.job) Job().save(newjob.job) # Inform Client of new Job added in inactive state - Notification().createNotification( + Notification( type='job_status', data=newjob.job, user=user, - expires=datetime.now() + timedelta(seconds=30), - ) + ).flush() return newjob.job + def training_output_folder(user: types.GirderUserModel) -> types.GirderModel: """Ensure that the user has a training results folder.""" viameFolder = Folder().createFolder( @@ -688,7 +697,7 @@ def postprocess( newjob.job[constants.JOBCONST_DATASET_ID] = dsFolder["_id"] Job().save(newjob.job) created_job_ids.append(newjob.job['_id']) - + elif imageItems.count() > 0: dsFolder["meta"][constants.DatasetMarker] = True elif largeImageItems.count() > 0: diff --git a/server/dive_server/event.py b/server/dive_server/event.py index 79a32d288..fabb02507 100644 --- a/server/dive_server/event.py +++ b/server/dive_server/event.py @@ -1,11 +1,10 @@ -from datetime import datetime, timedelta +from datetime import datetime, timedelta, timezone +import logging import os from bson.objectid import ObjectId import cherrypy -from girder import logger from girder.api.rest import getApiUrl -from girder.models.collection import Collection from girder.models.folder import Folder from girder.models.item import Item from girder.models.setting import Setting @@ -14,7 +13,7 @@ from girder.settings import SettingKey from girder.utility.mail_utils import renderTemplate, sendMail from girder_jobs.models.job import Job -from girder_worker.girder_plugin.utils import getWorkerApiUrl +from girder_plugin_worker.utils import getWorkerApiUrl from dive_tasks.dive_batch_postprocess import DIVEBatchPostprocessTaskParams from dive_utils import asbool, fromMeta @@ -35,6 +34,8 @@ videoRegex, ) +logger = logging.getLogger(__name__) + def send_new_user_email(event): try: @@ -80,8 +81,13 @@ def process_assetstore_import(event, meta: dict): foldername = base_name # resuse existing folder if it already exists with same name dest = Folder().createFolder(parentFolder, foldername, creator=user, reuseExisting=True) - now = datetime.now() - if now - dest['created'] > timedelta(hours=1): + created = dest['created'] + if getattr(created, 'tzinfo', None) is None: + created = created.replace(tzinfo=timezone.utc) + else: + created = created.astimezone(timezone.utc) + now = datetime.now(timezone.utc) + if now - created > timedelta(hours=1): # Remove the old referenced item, replace it with the new one. oldItem = Item().findOne({'folderId': dest['_id'], 'name': item['name']}) if oldItem is not None: @@ -137,7 +143,9 @@ def process_assetstore_import(event, meta: dict): folder["meta"].update( { TypeMarker: dataset_type, # Sets to video - FPSMarker: -1 if dataset_type == VideoType else 1, # -1 for video and 1 for image sequence + FPSMarker: ( + -1 if dataset_type == VideoType else 1 + ), # -1 for video and 1 for image sequence AssetstoreSourcePathMarker: root, MarkForPostProcess: True, # skip transcode or transcode if required **meta, @@ -163,7 +171,9 @@ def process_dangling_annotation_files(folder, user): continue # Check if the corresponding video folder exists base_name = os.path.splitext(item['name'])[0] - video_folder = Folder().findOne({'parentId': parent_folder_id, 'name': base_name, f'meta.{TypeMarker}': VideoType}) + video_folder = Folder().findOne( + {'parentId': parent_folder_id, 'name': base_name, f'meta.{TypeMarker}': VideoType} + ) if video_folder is not None: # Move the annotation file into the video folder item['meta'][AnnotationFileFutureProcessMarker] = False @@ -174,6 +184,14 @@ def process_dangling_annotation_files(folder, user): process_dangling_annotation_files(child, user) +def _job_cherrypy_callback_url() -> str: + """REST handlers have a CherryPy request; Celery workers do not.""" + try: + return cherrypy.url() + except Exception: + return getWorkerApiUrl() + + def convert_video_recursive(folder, user): token = Token().createToken(user=user, days=2) @@ -192,45 +210,44 @@ def convert_video_recursive(folder, user): job = Job().createLocalJob( module='dive_tasks.dive_batch_postprocess', function='batchPostProcessingTaskLauncher', - kwargs={'params': dive_batch_postprocess_task_params, 'url': cherrypy.url()}, + kwargs={'params': dive_batch_postprocess_task_params, 'url': _job_cherrypy_callback_url()}, title='Batch process Dive Batch Postprocess', type='DIVE Batch Postprocess', user=user, public=True, asynchronous=True, ) - job = Job().save(job) - Job().scheduleJob(job) - - - - -class DIVES3Imports: - destinationId = None - destinationType = None - - def process_s3_import_before(self, event): - self.destinationId = event.info.get('params', {}).get('destinationId') - self.destinationType = event.info.get('params', {}).get('destinationType') - - def process_s3_import_after(self, event): - if self.destinationType == 'folder' and self.destinationId is not None: - # go through all sub folders and add a new script to convert - destinationFolder = Folder().findOne({"_id": ObjectId(self.destinationId)}) - userId = destinationFolder['creatorId'] or destinationFolder['baseParentId'] - user = User().findOne({'_id': ObjectId(userId)}) - process_dangling_annotation_files(destinationFolder, user) - convert_video_recursive(destinationFolder, user) - if self.destinationType == 'collection' and self.destinationId is not None: - destinationCollection = Collection().findOne({"_id": ObjectId(self.destinationId)}) - userId = destinationCollection['creatorId'] or destinationCollection['baseParentId'] - user = User().findOne({'_id': ObjectId(userId)}) - child_folders = Folder().find({'parentId': ObjectId(self.destinationId)}) - for child in child_folders: - process_dangling_annotation_files(child, user) - convert_video_recursive(child, user) - self.destinationId = None - self.destinationType = None + # Run on the ``local`` Celery queue instead of scheduleLocal + daemon thread. + # importDataTask completes right after this; a daemon thread is often killed or + # never updates the job, so the document stays INACTIVE. + from dive_tasks.local_tasks import run_batch_postprocess_job + + run_batch_postprocess_job.delay(str(job['_id'])) + + +def run_post_assetstore_import(event): + """ + Run after Assetstore.importData completes. + + Bound on Celery ``local`` workers via ``dive_tasks.worker_girder_events``. + Admin and bucket-notification imports both run import in that process, not on Girder web. + """ + info = event.info + parent = info.get('parent') + parentType = info.get('parentType') + user = info.get('user') + if not parent or not parentType or not user: + return + userId = parent['creatorId'] or parent['baseParentId'] + owner = User().findOne({'_id': ObjectId(userId)}) + if parentType == 'folder': + process_dangling_annotation_files(parent, owner) + convert_video_recursive(parent, owner) + elif parentType in ('collection', 'user'): + child_folders = Folder().find({'parentId': parent['_id']}) + for child in child_folders: + process_dangling_annotation_files(child, owner) + convert_video_recursive(child, owner) def process_fs_import(event): diff --git a/server/dive_server/views_override.py b/server/dive_server/views_override.py index d191896e4..44629771a 100644 --- a/server/dive_server/views_override.py +++ b/server/dive_server/views_override.py @@ -1,12 +1,13 @@ """adds functionality to existing girder views""" import types + from girder.api import access from girder.api.describe import Description, autoDescribeRoute -from girder.api.rest import boundHandler, Resource +from girder.api.rest import Resource, boundHandler from girder.constants import AccessType, SortDir, TokenScope -from girder.models.user import User from girder.models.folder import Folder +from girder.models.user import User from girder_jobs.models import job from girder_worker.utils import JobStatus @@ -14,6 +15,7 @@ from . import crud_override + @access.user @boundHandler @autoDescribeRoute( @@ -67,6 +69,7 @@ def countJobs(self): 'outstanding': outstanding, } + @access.user @autoDescribeRoute( Description("List shared folders to the user.") @@ -80,20 +83,12 @@ def countJobs(self): required=False, ) ) -def list_shared_folders( - limit: int, - offset: int, - sort, - onlyNonAccessibles: bool -): +def list_shared_folders(limit: int, offset: int, sort, onlyNonAccessibles: bool): return crud_override.list_shared_folders( - Resource().getCurrentUser(), - limit, - offset, - sort, - onlyNonAccessibles + Resource().getCurrentUser(), limit, offset, sort, onlyNonAccessibles ) + @access.user @autoDescribeRoute( Description("Get the path to the root, or closest shared parent, of the folder's hierarchy.") @@ -102,7 +97,4 @@ def list_shared_folders( .errorResponse('Read access was denied for the folder.', 403) ) def get_root_path_or_relative(folder): - return crud_override.get_root_path_or_relative( - Resource().getCurrentUser(), - folder - ) \ No newline at end of file + return crud_override.get_root_path_or_relative(Resource().getCurrentUser(), folder) diff --git a/server/dive_server/views_rpc.py b/server/dive_server/views_rpc.py index 57cfc47b0..d06aaa948 100644 --- a/server/dive_server/views_rpc.py +++ b/server/dive_server/views_rpc.py @@ -60,7 +60,7 @@ def __init__(self, resourceName): def run_pipeline_task(self, folder, forceTranscoded, pipeline: PipelineDescription, pipelineParams: dict[str, str]): worker_capabilities.require_pipeline_worker() return crud_rpc.run_pipeline(self.getCurrentUser(), folder, pipeline, forceTranscoded, pipelineParams) - + @access.user @autoDescribeRoute( Description("Export pipeline to ONNX") diff --git a/server/dive_tasks/__init__.py b/server/dive_tasks/__init__.py index 761a91a48..48e53f38f 100644 --- a/server/dive_tasks/__init__.py +++ b/server/dive_tasks/__init__.py @@ -12,4 +12,9 @@ def __init__(self, app, *args, **kwargs): def task_imports(self): # Return a list of python importable paths to the # plugin's path directory - return ["dive_tasks.tasks"] + # worker_girder_events first: bind Girder handlers before any task module loads. + return [ + 'dive_tasks.worker_girder_events', + 'dive_tasks.tasks', + 'dive_tasks.local_tasks', + ] diff --git a/server/dive_tasks/celeryconfig.py b/server/dive_tasks/celeryconfig.py index 0bd3f2d2d..81b0daee4 100644 --- a/server/dive_tasks/celeryconfig.py +++ b/server/dive_tasks/celeryconfig.py @@ -9,7 +9,7 @@ dive_username = os.environ.get('DIVE_USERNAME', None) dive_password = os.environ.get('DIVE_PASSWORD', None) dive_api_url = os.environ.get('DIVE_API_URL', 'https://viame.kitware.com/api/v1') -broker_url = os.environ.get('CELERY_BROKER_URL', None) +broker_url = os.environ.get('GIRDER_WORKER_BROKER', None) if dive_username and dive_password: info( @@ -42,7 +42,7 @@ task_default_queue = queue_name if broker_url is None: - raise RuntimeError('CELERY_BROKER_URL must be set') + raise RuntimeError('GIRDER_WORKER_BROKER must be set') worker_send_task_events = False # https://docs.celeryproject.org/en/stable/userguide/configuration.html#std-setting-worker_prefetch_multiplier diff --git a/server/dive_tasks/dive_batch_postprocess.py b/server/dive_tasks/dive_batch_postprocess.py index 9238ef5eb..f1a0bbbf4 100644 --- a/server/dive_tasks/dive_batch_postprocess.py +++ b/server/dive_tasks/dive_batch_postprocess.py @@ -284,4 +284,4 @@ def _get_folder_name(gc: GirderClient, folder_id: str) -> str: folder = gc.getFolder(folder_id) return folder.get('name', folder_id) except Exception: - return folder_id \ No newline at end of file + return folder_id diff --git a/server/dive_tasks/local_tasks.py b/server/dive_tasks/local_tasks.py new file mode 100644 index 000000000..b60e58842 --- /dev/null +++ b/server/dive_tasks/local_tasks.py @@ -0,0 +1,62 @@ +""" +Celery tasks bound to the ``local`` queue (same queue as Girder's ``importDataTask``). + +Kept separate from ``tasks.py`` so the main worker task module stays focused on +GPU/default-queue work. +""" + +from girder_worker.app import app + + +@app.task(queue='local', acks_late=True, ignore_result=True) +def run_batch_postprocess_job(job_id: str): + """ + Run DIVE batch postprocess for an existing Girder job document. + + Scheduled on ``local`` so this runs in a normal Celery task instead of a + daemon thread spawned from ``scheduleLocal``. A thread started when the + import task is finishing is unreliable and often leaves the parent job + stuck in INACTIVE. + """ + from girder_jobs.models.job import Job + + from dive_tasks.dive_batch_postprocess import batch_postprocess_task + + job = Job().load(job_id, force=True) + batch_postprocess_task(job) + + +@app.task(queue='local', acks_late=True, ignore_result=True) +def import_assetstore_path_async( + assetstore_id: str, + parent_id: str, + parent_type: str, + import_path: str, + user_id: str, + *, + force_recursive: bool = False, + leaf_folders_as_items: bool = False, +): + """ + Run ``Assetstore.importData`` on the ``local`` queue (e.g. GCS bucket notifications). + + Keeps ``force_recursive=False`` for incremental object notifications; Girder's + ``importDataTask`` does not forward that flag and defaults to full recursion. + """ + from girder.models.assetstore import Assetstore + from girder.models.user import User + from girder.utility.model_importer import ModelImporter + + user = User().load(user_id, force=True) + assetstore = Assetstore().load(assetstore_id) + parent = ModelImporter.model(parent_type).load(parent_id, force=True) + Assetstore().importData( + assetstore, + parent, + parent_type, + {'importPath': import_path}, + None, + user, + force_recursive=force_recursive, + leafFoldersAsItems=leaf_folders_as_items, + ) diff --git a/server/dive_tasks/tasks.py b/server/dive_tasks/tasks.py index 5485f706e..cbcff2dca 100644 --- a/server/dive_tasks/tasks.py +++ b/server/dive_tasks/tasks.py @@ -21,7 +21,13 @@ from dive_tasks.manager import patch_manager from dive_tasks.pipeline_discovery import discover_configs from dive_utils import constants, fromMeta -from dive_utils.types import AvailableJobSchema, GirderModel, PipelineJob, TrainingJob, ExportTrainedPipelineJob +from dive_utils.types import ( + AvailableJobSchema, + ExportTrainedPipelineJob, + GirderModel, + PipelineJob, + TrainingJob, +) EMPTY_JOB_SCHEMA: AvailableJobSchema = { 'pipelines': {}, diff --git a/server/dive_tasks/worker_girder_events.py b/server/dive_tasks/worker_girder_events.py new file mode 100644 index 000000000..cd30e890f --- /dev/null +++ b/server/dive_tasks/worker_girder_events.py @@ -0,0 +1,46 @@ +""" +Register Girder model events on the Celery worker. + +Assetstore imports run in ``importDataTask`` and ``import_assetstore_path_async`` (queue +``local``). Those processes do not load Girder server plugins, so per-file and post-import +handlers are registered here instead of in ``dive_server``. + +``run_post_assetstore_import`` schedules local Girder jobs (e.g. batch postprocess). Those +jobs only leave ``INACTIVE`` when ``jobs.schedule`` is handled; the Jobs plugin registers +that on the web server, so we bind the same handler here. +""" + +from girder import events +from girder_jobs import scheduleLocal + +from dive_server.event import ( + process_fs_import, + process_s3_import, + run_post_assetstore_import, +) + + +def _register(): + events.bind( + 's3_assetstore_imported', + 'dive_worker_s3_assetstore_imported', + process_s3_import, + ) + events.bind( + 'filesystem_assetstore_imported', + 'dive_worker_filesystem_assetstore_imported', + process_fs_import, + ) + events.bind( + 'assetstore_import.after', + 'dive_worker_assetstore_import_after', + run_post_assetstore_import, + ) + events.bind( + 'jobs.schedule', + 'dive_worker_jobs_schedule_local', + scheduleLocal, + ) + + +_register() diff --git a/server/pyproject.toml b/server/pyproject.toml index b1d860ad3..22125f844 100644 --- a/server/pyproject.toml +++ b/server/pyproject.toml @@ -34,17 +34,16 @@ classifiers = [ "Natural Language :: English", "Programming Language :: Python", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.11", ] -requires-python = ">=3.8,<3.12" +requires-python = ">=3.10,<3.12" dependencies = [ - "cheroot>=8.4.5", "click>=8.1.3", - "girder>=3.2.8,<4", - "girder_jobs>=3.2.8,<4", - "girder_worker>=0.10.3,<1", + "girder==5.0.4", + "girder_jobs==5.0.4", + "girder_worker==5.0.4", + "girder-plugin-worker==5.0.4", "girder_worker_utils>=0.9.0,<1", "pydantic==1.10.13", "pyrabbit2==1.0.7", @@ -54,7 +53,8 @@ dependencies = [ "urllib3<1.27", "bitarray>=2.9.2", "simplejpeg>=1.7.2", - "girder-large-image>=1.28.1,<1.30", + "large-image==1.34.2a180", + "girder-large-image==1.34.2a180", "cherrypy>=18.9.0", "numpy==1.24.4", ] @@ -67,14 +67,14 @@ dev = [ [project.optional-dependencies] large-image = [ - "large-image>=1.28.1,<1.30", - "large-image-tasks>=1.28.1,<1.30", - "large-image-converter>=1.28.1,<1.30", - "large-image-source-pil>=1.28.1,<1.30", - "large-image-source-gdal>=1.28.1,<1.30", - "large-image-source-tiff>=1.28.1,<1.30", - "large-image-source-ometiff>=1.28.1,<1.30", - "large-image-source-openjpeg>=1.28.1,<1.30", + "large-image", + "large-image-tasks", + "large-image-converter", + "large-image-source-pil", + "large-image-source-gdal", + "large-image-source-tiff", + "large-image-source-ometiff", + "large-image-source-openjpeg", "gdal", "pylibtiff", ] @@ -116,6 +116,7 @@ allow-direct-references = true [tool.uv] conflicts = [] +prerelease = "allow" [[tool.uv.index]] name = "large_image_wheels" diff --git a/server/rabbitmq_user_queues/views.py b/server/rabbitmq_user_queues/views.py index 21498f3fb..4c522a6da 100644 --- a/server/rabbitmq_user_queues/views.py +++ b/server/rabbitmq_user_queues/views.py @@ -1,7 +1,7 @@ +import logging from typing import Optional import uuid -from girder import logger from girder.api import access from girder.api.describe import Description, autoDescribeRoute from girder.api.rest import Resource @@ -13,6 +13,8 @@ from .constants import UserQueueMarker from .models import Settings, UserQueueModel +logger = logging.getLogger(__name__) + class RabbitUserQueue(Resource): def __init__(self): diff --git a/server/uv.lock b/server/uv.lock index 3ca3b2867..97702fa00 100644 --- a/server/uv.lock +++ b/server/uv.lock @@ -1,21 +1,18 @@ version = 1 revision = 3 -requires-python = ">=3.8, <3.12" +requires-python = ">=3.10, <3.12" resolution-markers = [ "python_full_version >= '3.11' and sys_platform == 'darwin'", "python_full_version >= '3.11' and platform_machine == 'aarch64' and sys_platform == 'linux'", "(python_full_version >= '3.11' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version >= '3.11' and sys_platform != 'darwin' and sys_platform != 'linux')", - "python_full_version == '3.10.*' and sys_platform == 'darwin'", - "python_full_version == '3.10.*' and platform_machine == 'aarch64' and sys_platform == 'linux'", - "(python_full_version == '3.10.*' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version == '3.10.*' and sys_platform != 'darwin' and sys_platform != 'linux')", - "python_full_version == '3.9.*' and platform_machine == 'arm64' and sys_platform == 'darwin'", - "python_full_version == '3.9.*' and platform_machine == 'aarch64' and sys_platform == 'linux'", - "(python_full_version == '3.9.*' and platform_machine != 'arm64' and sys_platform == 'darwin') or (python_full_version == '3.9.*' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version == '3.9.*' and sys_platform != 'darwin' and sys_platform != 'linux')", - "python_full_version < '3.9' and platform_machine == 'arm64' and sys_platform == 'darwin'", - "python_full_version < '3.9' and platform_machine == 'aarch64' and sys_platform == 'linux'", - "(python_full_version < '3.9' and platform_machine != 'arm64' and 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