#14 Support Ubuntu 24.04

README.md

@@ -1,4 +1,95 @@
-# Functional Curation experiment runner for the Web Lab
+# FC experiment runner for the Web Lab
 
-Initially this is just the web service + Celery task queue from Web Lab version 1.
-It will be refactored and extended to support other backends as we progress.
+This repository implements a backend job runner for the WebLab’s [Functional Curation (FC)](https://github.com/ModellingWebLab/weblab-fc) experiments. It functions as an asynchronous execution service that bridges the WebLab frontend with long-running FC model/protocol runs, then reports status and artifacts back to the frontend.
+
+At a high level, it:
+
+1. Accepts experiment-related requests from a web-facing CGI endpoint.
+1. Queues work in [Celery](https://docs.celeryq.dev/).
+1. Downloads model/protocol archives (and optional fitting data/specs).
+1. Checks protocol-model compatibility.
+1. Runs the simulation/fitting executable.
+1. Zips results and posts them back to a callback URL.
+
+## Installation
+
+### Install dependencies
+
+Install [Functional Curation (FC)](https://github.com/ModellingWebLab/weblab-fc).
+
+Install additional dependencies
+```bash
+python3 -m pip install -r requirements/base.txt
+```
+
+Update configuration settings in `fcws/config.json`
+
+### Install service
+
+Install a Celery service. For example, save this to `/etc/systemd/system/celery.service`:
+
+```txt
+[Unit]
+Description=Celery Service
+After=network.target
+
+[Service]
+Type=forking
+User=celery
+Group=celery
+EnvironmentFile=-/etc/default/celery
+
+WorkingDirectory=/path/to/fc-runner
+RuntimeDirectory=celery
+
+ExecStart=/bin/sh -c '${CELERY_BIN} multi start ${CELERYD_NODES} -A ${CELERY_APP} \
+  --pidfile=${CELERYD_PID_FILE} \
+  --logfile=${CELERYD_LOG_FILE} \
+  --loglevel=${CELERYD_LOG_LEVEL} ${CELERYD_OPTS}'
+
+ExecStop=/bin/sh -c '${CELERY_BIN} multi stopwait ${CELERYD_NODES} --pidfile=${CELERYD_PID_FILE}'
+
+ExecReload=/bin/sh -c '${CELERY_BIN} multi restart ${CELERYD_NODES} -A ${CELERY_APP} \
+  --pidfile=${CELERYD_PID_FILE} \
+  --logfile=${CELERYD_LOG_FILE} \
+  --loglevel=${CELERYD_LOG_LEVEL} ${CELERYD_OPTS}'
+
+Restart=on-failure
+
+[Install]
+WantedBy=multi-user.target
+```
+
+and save this to `/etc/default/celery`
+
+```txt
+# Configuration for Functional Curation celery daemon.
+
+# Number of worker nodes
+CELERYD_NODES=2
+
+# Path to celery executable
+CELERY_BIN=/path/to/bin/celery"
+
+# Celery application
+CELERY_APP="fcws.tasks:app"
+
+# Extra command-line arguments to the workers
+CELERYD_OPTS="--concurrency=2 -l info -Ofair --statedb=/var/lib/celery/%n.state -Q:1 admin -Q default,admin"
+
+CELERYD_LOG_FILE="/var/log/celery/%n%I.log"
+CELERYD_PID_FILE="/run/%n.pid"
+CELERYD_LOG_LEVEL="INFO"
+
+# Notes:
+# - The default queue is set to 'default' in celeryconfig.py, and admin users 
+#   use 'admin' (see fcws/__init__.py).
+# - %n will be replaced with the first part of the nodename.
+# - %I will be replaced with the current child process index
+#   and is important when using the prefork pool to avoid race conditions.
+```
+
+```sh
+sudo systemctl daemon-reload
+sudo systemctl start celery.service
+```

fcws/__init__.py

@@ -1,4 +1,6 @@
-# Back-end web service routines for the functional curation website
+"""
+Functional Curation web service (FCWS) back-end routines for the WebLab.
+"""
 
 import json
 import os

requirements/Makefile

@@ -6,7 +6,7 @@ outputs := $(objects:.in=.txt)
 all: $(outputs)
 
 %.txt: %.in
-	pip-compile -v -U --output-file $@ $<
+	pip-compile -v --strip-extras -U --output-file $@ $<
 
 test.txt: base.txt
 

requirements/base.in

@@ -1,4 +1,4 @@
 # We use auto-retry with exponential backoff
-celery>=4.2
+celery>=5.3
 
 requests

requirements/base.txt

@@ -1,38 +1,59 @@
 #
-# This file is autogenerated by pip-compile
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.10
+# by the following command:
 #
-#    pip-compile --output-file=base.txt base.in
+#    pip-compile --output-file=base.txt --strip-extras base.in
 #
-amqp==2.5.1
+amqp==5.3.1
     # via kombu
-billiard==3.6.1.0
+billiard==4.2.4
     # via celery
-celery==4.3.0
+celery==5.6.2
     # via -r base.in
-certifi==2019.9.11
+certifi==2026.2.25
     # via requests
-chardet==3.0.4
+charset-normalizer==3.4.6
     # via requests
-idna==2.8
+click==8.3.1
+    # via
+    #   celery
+    #   click-didyoumean
+    #   click-plugins
+    #   click-repl
+click-didyoumean==0.3.1
+    # via celery
+click-plugins==1.1.1.2
+    # via celery
+click-repl==0.3.0
+    # via celery
+exceptiongroup==1.3.1
+    # via celery
+idna==3.11
     # via requests
-importlib-metadata==0.23
-    # via kombu
-kombu==4.6.5
+kombu==5.6.2
     # via celery
-more-itertools==5.0.0
-    # via zipp
-pytz==2019.3
+packaging==26.0
+    # via kombu
+prompt-toolkit==3.0.52
+    # via click-repl
+python-dateutil==2.9.0.post0
     # via celery
-requests==2.22.0
+requests==2.32.5
     # via -r base.in
-six==1.12.0
-    # via more-itertools
-urllib3==1.25.8
+six==1.17.0
+    # via python-dateutil
+typing-extensions==4.15.0
+    # via exceptiongroup
+tzdata==2025.3
+    # via kombu
+tzlocal==5.3.1
+    # via celery
+urllib3==2.6.3
     # via requests
-vine==1.3.0
+vine==5.1.0
     # via
     #   amqp
     #   celery
-zipp==0.6.0
-    # via importlib-metadata
+    #   kombu
+wcwidth==0.6.0
+    # via prompt-toolkit