Merge branch 'develop' into dmoitzi/proms-and-vcf-icons-for-aevidence

Makefile

@@ -9,6 +9,10 @@ ruff = ruff check $(pkg_src) setup.py --line-length 140 --select E,W,F,N,I,C,B,U
 start:
 	python $(pkg_src)
 
+.PHONY: celery  ## Start the celery worker
+celery:
+	celery -A $(pkg_src).dev_celery worker --loglevel=INFO --concurrency=8 -O fair -P prefork
+
 .PHONY: all  ## Perform the most common development-time rules
 all: format lint test
 

docker-compose.yml

@@ -0,0 +1,8 @@
+version: '3.0'
+
+services:
+  redis:
+    image: redis:7.4-alpine
+    ports:
+      - '6379:6379'
+    command: redis-server --requirepass admin

requirements.txt

@@ -1,6 +1,8 @@
 # a2wsgi==1.6.0 # This WSIGMiddleware is not compatible with starlette_context
 alembic==1.13.2
 cachetools==5.3.3
+celery>=5.0.0,<6.0.0
+celery-types~=0.22.0
 fastapi==0.112.2
 json-cfg==0.4.2
 openpyxl==3.1.5
@@ -18,9 +20,10 @@ psycopg==3.2.1
 psycopg2==2.9.9
 pydantic==1.10.17
 pyjwt[crypto]==2.9.0
-pytest-postgresql==6.0.1
+pytest-postgresql==6.1.1
 python-dateutil==2.9.0.post0
 requests==2.32.3
+redis>=5.0.0,<6.0.0
 sentry-sdk~=2.13.0
 SQLAlchemy>=1.4.40,<=1.4.53
 starlette-context==0.3.6

src/vis/bar/BarChart.tsx

@@ -417,6 +417,7 @@ export function BarChart({
                 scrollHideDelay={0}
                 offsetScrollbars
               >
+                {/* @ts-ignore */}
                 <VariableSizeList
                   height={containerHeight - CHART_HEIGHT_MARGIN / 2}
                   itemCount={filteredUniqueFacetVals.length}

visyn_core/celery/app.py

@@ -0,0 +1,44 @@
+import logging
+import logging.config
+
+from celery import Celery
+
+from ..plugin.parser import EntryPointPlugin
+
+
+def init_celery_manager(*, plugins: list[EntryPointPlugin]):
+    """
+    Create a new Celery app and initialize it with the given plugins.
+    """
+    from .. import manager
+
+    _log = logging.getLogger(__name__)
+
+    if not manager.settings.visyn_core.celery:
+        _log.warning("No Celery settings found in configuration, skipping Celery initialization")
+        return None
+
+    manager.celery = Celery("visyn", **manager.settings.visyn_core.celery)
+
+    _log.info("Initializing celery app")
+
+    # Discover tasks from all plugins, i.e. visyn_core.tasks, visyn_plugin.tasks
+    manager.celery.autodiscover_tasks([p.id for p in plugins])
+
+    return manager.celery
+
+
+def create_celery_worker_app(*, workspace_config: dict | None = None):
+    """
+    Create a new Celery app in standalone mode, i.e. without a FastAPI instance.
+    """
+    from .. import manager
+    from ..server.visyn_server import create_visyn_server
+
+    # Create the whole FastAPI instance to ensure that the configuration and plugins are loaded, extension points are registered, database migrations are executed, ...
+    create_visyn_server(workspace_config=workspace_config)
+
+    _log = logging.getLogger(__name__)
+    _log.info("Starting celery worker")
+
+    return init_celery_manager(plugins=manager.registry.plugins)

visyn_core/celery/main.py

@@ -0,0 +1,3 @@
+from .app import create_celery_worker_app
+
+celery_app = create_celery_worker_app()

visyn_core/dev_app.py

@@ -1,10 +1,8 @@
-import os
+import pathlib
 import sys
 
 from .server.visyn_server import create_visyn_server
 
 # This app is either started via the uvicorn runner in __main__.py,
 # or as module to execute commands via `python -m <app>.dev_app db-migration exec ...`
-app = create_visyn_server(
-    start_cmd=" ".join(sys.argv[1:]), workspace_config={"_env_file": os.path.join(os.path.dirname(os.path.realpath(__file__)), ".env")}
-)
+app = create_visyn_server(start_cmd=" ".join(sys.argv[1:]), workspace_config={"_env_file": pathlib.Path(__file__).parent / ".env"})

visyn_core/dev_celery.py

@@ -0,0 +1,5 @@
+import pathlib
+
+from .celery.app import create_celery_worker_app
+
+celery_app = create_celery_worker_app(workspace_config={"_env_file": pathlib.Path(__file__).parent / ".env"})

visyn_core/manager.py

@@ -5,17 +5,24 @@
 # Additionally, we have to wrap our types/classes in '', such that they are evaluated lazily.
 # See https://peps.python.org/pep-0563/#runtime-annotation-resolution-and-type-checking for more information.
 if TYPE_CHECKING:
+    # Monkey-patch Celery to support proper type hints: https://pypi.org/project/celery-types/
+    from celery.app.task import Task
+
+    from .celery.app import Celery
     from .dbmanager import DBManager
     from .dbmigration.manager import DBMigrationManager
     from .id_mapping.manager import MappingManager
     from .plugin.registry import Registry
     from .security.manager import SecurityManager
     from .settings.model import GlobalSettings
 
+    Task.__class_getitem__ = classmethod(lambda cls, *args, **kwargs: cls)  # type: ignore[attr-defined]
+
 
 db: "DBManager" = None  # type: ignore
 db_migration: "DBMigrationManager" = None  # type: ignore
 id_mapping: "MappingManager" = None  # type: ignore
 security: "SecurityManager" = None  # type: ignore
 registry: "Registry" = None  # type: ignore
 settings: "GlobalSettings" = None  # type: ignore
+celery: "Celery" = None  # type: ignore

visyn_core/server/utils.py

@@ -1,9 +1,12 @@
 import http
 import logging
+import logging.config
 import time
 import traceback
 
 from fastapi import HTTPException
+from pydantic import create_model
+from pydantic.utils import deep_update
 
 from .. import manager
 
@@ -17,6 +20,44 @@
 _log = logging.getLogger(__name__)
 
 
+def init_settings_manager(workspace_config: dict | None = None):
+    from ..settings.model import GlobalSettings
+    from ..settings.utils import load_workspace_config
+
+    # Load the workspace config.json and initialize the global settings
+    workspace_config = workspace_config if isinstance(workspace_config, dict) else load_workspace_config()
+    # Temporary backwards compatibility: if no visyn_core config entry is found, copy the one from tdp_core.
+    if "visyn_core" not in workspace_config and "tdp_core" in workspace_config:
+        logging.warn('You are still using "tdp_core" config entries instead of "visyn_core" entries. Please migrate as soon as possible!')
+        workspace_config["visyn_core"] = workspace_config["tdp_core"]
+
+    manager.settings = GlobalSettings(**workspace_config)
+
+    # Initialize the logging
+    logging_config = manager.settings.visyn_core.logging
+
+    if manager.settings.visyn_core.log_level:
+        try:
+            logging_config["root"]["level"] = manager.settings.visyn_core.log_level
+        except KeyError:
+            logging.warn("You have set visyn_core.log_level, but no root logger is defined in visyn_core.logging")
+
+    logging.config.dictConfig(logging_config)
+
+    # Load the initial plugins
+    from ..plugin.parser import get_config_from_plugins, load_all_plugins
+
+    plugins = load_all_plugins()
+
+    # With all the plugins, load the corresponding configuration files and create a new model based on the global settings, with all plugin models as sub-models
+    [plugin_config_files, plugin_settings_models] = get_config_from_plugins(plugins)
+    visyn_server_settings = create_model("VisynServerSettings", __base__=GlobalSettings, **plugin_settings_models)  # type: ignore
+    # Patch the global settings by instantiating the new settings model with the global config, all config.json(s), and pydantic models
+    manager.settings: GlobalSettings = visyn_server_settings(**deep_update(*plugin_config_files, workspace_config))  # type: ignore
+
+    return plugins
+
+
 init_legacy_app = None
 try:
     # Flask is an optional dependency and must be added to the requirements for legacy apps.

visyn_core/server/visyn_server.py

@@ -4,21 +4,13 @@
 import threading
 from typing import Any
 
-from fastapi import FastAPI
-from fastapi.middleware.wsgi import WSGIMiddleware
-from pydantic import create_model
-from pydantic.utils import deep_update
-from starlette_context.middleware import RawContextMiddleware
-
 from ..settings.constants import default_logging_dict
 
 # Initialize the logging very early as otherwise the already created loggers receive a default loglevel WARN, leading to logs not being shown.
 logging.config.dictConfig(default_logging_dict)
 
 
-def create_visyn_server(
-    *, fast_api_args: dict[str, Any] | None = None, start_cmd: str | None = None, workspace_config: dict | None = None
-) -> FastAPI:
+def create_visyn_server(*, fast_api_args: dict[str, Any] | None = None, start_cmd: str | None = None, workspace_config: dict | None = None):
     """
     Create a new FastAPI instance while ensuring that the configuration and plugins are loaded, extension points are registered, database migrations are executed, ...
 
@@ -30,48 +22,14 @@ def create_visyn_server(
     if fast_api_args is None:
         fast_api_args = {}
     from .. import manager
-    from ..settings.model import GlobalSettings
-    from ..settings.utils import load_workspace_config
-
-    # Load the workspace config.json and initialize the global settings
-    workspace_config = workspace_config if isinstance(workspace_config, dict) else load_workspace_config()
-    # Temporary backwards compatibility: if no visyn_core config entry is found, copy the one from tdp_core.
-    if "visyn_core" not in workspace_config and "tdp_core" in workspace_config:
-        logging.warn('You are still using "tdp_core" config entries instead of "visyn_core" entries. Please migrate as soon as possible!')
-        workspace_config["visyn_core"] = workspace_config["tdp_core"]
-
-    manager.settings = GlobalSettings(**workspace_config)
-
-    # Initialize the logging
-    logging_config = manager.settings.visyn_core.logging
-
-    if manager.settings.visyn_core.log_level:
-        try:
-            logging_config["root"]["level"] = manager.settings.visyn_core.log_level
-        except KeyError:
-            logging.warn("You have set visyn_core.log_level, but no root logger is defined in visyn_core.logging")
-
-    logging.config.dictConfig(logging_config)
+    from .utils import init_settings_manager
 
-    # Filter out the metrics endpoint from the access log
-    class EndpointFilter(logging.Filter):
-        def filter(self, record: logging.LogRecord) -> bool:
-            return "GET /api/metrics" and "GET /api/health" and "GET /metrics" and "GET /health" not in record.getMessage()
-
-    logging.getLogger("uvicorn.access").addFilter(EndpointFilter())
+    plugins = init_settings_manager(workspace_config=workspace_config)
 
     _log = logging.getLogger(__name__)
-    _log.info(f"Starting visyn_server in {manager.settings.env} mode")
+    _log.info(f"Starting in {manager.settings.env} mode")
 
-    # Load the initial plugins
-    from ..plugin.parser import get_config_from_plugins, load_all_plugins
-
-    plugins = load_all_plugins()
-    # With all the plugins, load the corresponding configuration files and create a new model based on the global settings, with all plugin models as sub-models
-    [plugin_config_files, plugin_settings_models] = get_config_from_plugins(plugins)
-    visyn_server_settings = create_model("VisynServerSettings", __base__=GlobalSettings, **plugin_settings_models)  # type: ignore
-    # Patch the global settings by instantiating the new settings model with the global config, all config.json(s), and pydantic models
-    manager.settings = visyn_server_settings(**deep_update(*plugin_config_files, workspace_config))
+    from fastapi import FastAPI
 
     app = FastAPI(
         debug=manager.settings.is_development_mode,
@@ -84,6 +42,13 @@ def filter(self, record: logging.LogRecord) -> bool:
         **fast_api_args,
     )
 
+    # Filter out the metrics endpoint from the access log
+    class EndpointFilter(logging.Filter):
+        def filter(self, record: logging.LogRecord) -> bool:
+            return "GET /api/metrics" and "GET /api/health" and "GET /metrics" and "GET /health" not in record.getMessage()
+
+    logging.getLogger("uvicorn.access").addFilter(EndpointFilter())
+
     from ..middleware.exception_handler_middleware import ExceptionHandlerMiddleware
 
     # TODO: For some reason, a @app.exception_handler(Exception) is not called here. We use a middleware instead.
@@ -113,6 +78,10 @@ def filter(self, record: logging.LogRecord) -> bool:
         )
 
     # Initialize global managers.
+    from ..celery.app import init_celery_manager
+
+    app.state.celery = init_celery_manager(plugins=plugins)
+
     from ..plugin.registry import Registry
 
     app.state.registry = manager.registry = Registry()
@@ -149,6 +118,8 @@ def filter(self, record: logging.LogRecord) -> bool:
         sys.exit(0)
 
     # Load all namespace plugins as WSGIMiddleware plugins
+    from fastapi.middleware.wsgi import WSGIMiddleware
+
     from .utils import init_legacy_app, load_after_server_started_hooks
 
     namespace_plugins = manager.registry.list("namespace")
@@ -203,6 +174,8 @@ async def change_anyio_total_tokens():
 
     init_client_config(app)
 
+    from starlette_context.middleware import RawContextMiddleware
+
     from ..middleware.request_context_plugin import RequestContextPlugin
 
     # Use starlette-context to store the current request globally, i.e. accessible via context['request']

visyn_core/settings/model.py

@@ -180,6 +180,10 @@ class VisynCoreSettings(BaseModel):
     """
     sentry: SentrySettings = SentrySettings()
     """
+    Settings for celery. If not set, celery will not be initialized.
+    """
+    celery: dict[str, Any] | None = None
+    """
     Settings for Sentry. DSN will be shared via the client config.
     """
     cypress: bool = False

visyn_core/tests/fixtures/app.py

@@ -23,7 +23,13 @@ def mock_current_user_in_manager(self):
 @pytest.fixture()
 def workspace_config() -> dict:
     return {
-        "visyn_core": {"enabled_plugins": ["visyn_core"]},
+        "visyn_core": {
+            "enabled_plugins": ["visyn_core"],
+            "celery": {
+                "broker": "memory://localhost/",
+                "task_always_eager": True,
+            },
+        },
     }
 
 

visyn_core/tests/test_celery.py

@@ -0,0 +1,13 @@
+from fastapi.testclient import TestClient
+
+from visyn_core import manager
+
+
+def test_celery_worker(client: TestClient):
+
+    @manager.celery.task
+    def add(x, y):
+        return x + y
+
+    result = add.delay(2, 4)
+    assert result.get(timeout=1) == 6