Merge branch 'main' into mwmvisit

README.md

@@ -49,6 +49,8 @@ uvicorn valis.wsgi:app --reload
 ```
 This will start a local web server at `http://localhost:8000/valis/`.  The API documentation will be located at `http://localhost:8000/valis/docs`.  Or to see the alternate documentation, go to `http://localhost:8000/valis/redoc/`
 
+By default, the app will try to cache some route responses to a Redis database in localhost. If you don't have a Redis instance running you can use `in-memory` for testing (this caches the response directly in RAM). To do so, edit `~/.config/sdss/valis.yaml` and add `cache_backend: in-memory` (this should only be used in development or it could quickly use all available memory; the memory is freed when the app is stopped). Caching can be completely disabled by setting `cache_backend: null`. The time the cache is kept can be set with the `cache_ttl` (time to live) setting option.
+
 ### Database Connection
 
 Valis uses the `sdssdb` package for all connections to databases.  The most relevant database for the API is the `sdss5db` on `pipelines.sdss.org`.  The easiest way to connect is through a local SSH tunnel. To set up a tunnel,
@@ -91,8 +93,9 @@ Additionally, you can set the environment variable `VALIS_DB_RESET=false` or add
 ## Deployment
 
 This section describes a variety of deployment methods.  Valis uses gunicorn as its
-wsgi http server. It binds the app both to port 8000, and a unix socket.  The defaut mode
-is to start valis with an awsgi uvicorn server, with 4 workers.
+wsgi http server. It binds the app both to port 8000, and a unix socket.  The default mode is to start valis with an awsgi uvicorn server, with 4 workers.
+
+Valis requires a Redis database running at the default location in `localhost:6379`.  If this is not possible, caching can be done in memory by modifying `~/.config/sdss/valis.yaml` to use `cache_backend: in-memory`.
 
 ### Deploying Zora + Valis together
 See the SDSS [Zora+Valis Docker](https://github.com/sdss/zora_valis_dockers) repo page.

pyproject.toml

@@ -50,6 +50,7 @@ deepmerge = "^1.1.1"
 fuzzy-types = "^0.1.3"
 sdss-solara = {git = "https://github.com/sdss/sdss_solara.git", rev = "main", optional = true}
 markdown = "^3.7"
+fastapi-cache2 = { version = "^0.2.2", extras = ["redis"] }
 
 [tool.poetry.dev-dependencies]
 ipython = ">=7.11.0"

python/valis/cache.py

@@ -0,0 +1,363 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Filename: main.py
+# Project: app
+# Author: José Sánchez-Gallego
+# Created: Monday, 9th December 2024
+# License: BSD 3-clause "New" or "Revised" License
+# Copyright (c) 2020 José Sánchez-Gallego
+# Last Modified: Monday, 9th December 2024
+# Modified By: José Sánchez-Gallego
+
+from __future__ import annotations
+
+import base64
+import hashlib
+import json
+import logging
+import re
+import orjson
+from contextlib import asynccontextmanager
+from functools import wraps
+from inspect import Parameter, isawaitable, iscoroutinefunction
+from typing import (
+    TYPE_CHECKING,
+    Any,
+    Awaitable,
+    Callable,
+    List,
+    Optional,
+    ParamSpec,
+    Tuple,
+    Type,
+    TypeVar,
+    Union,
+    cast
+)
+
+from fastapi.concurrency import run_in_threadpool
+from fastapi.dependencies.utils import (
+    get_typed_return_annotation,
+    get_typed_signature
+)
+from fastapi_cache import Backend, Coder, FastAPICache
+from fastapi_cache.backends.inmemory import InMemoryBackend
+from fastapi_cache.backends.redis import RedisBackend
+from fastapi_cache.decorator import _augment_signature, _locate_param
+from redis.asyncio.client import Redis as RedisAsync
+from redis.client import Redis
+from starlette.requests import Request
+from starlette.responses import Response
+from starlette.status import HTTP_304_NOT_MODIFIED
+
+from valis.settings import settings
+
+
+if TYPE_CHECKING:
+    from typing import AsyncIterator
+
+    from fastapi import FastAPI
+    from fastapi_cache.coder import Coder
+    from fastapi_cache.types import KeyBuilder
+
+
+__all__ = ['valis_cache', 'lifespan', 'valis_cache_key_builder']
+
+
+P = ParamSpec("P")
+R = TypeVar("R")
+
+
+logger = logging.getLogger("uvicorn.error")
+
+
+def bdefault(obj):
+    """ Custom encoder for orjson """
+    # handle python memoryview objects
+    if isinstance(obj, memoryview):
+        return base64.b64encode(obj.tobytes()).decode()
+    raise TypeError
+
+
+class ORJsonCoder(Coder):
+    """ Custom encoder class for the cache that uses orjson """
+
+    @classmethod
+    def encode(cls, value: Any) -> bytes:
+        """ serialization """
+        return orjson.dumps(
+            value,
+            default=bdefault,
+            option=orjson.OPT_SERIALIZE_NUMPY,
+        )
+
+    @classmethod
+    def decode(cls, value: bytes) -> Any:
+        """ deserialization """
+        return orjson.loads(value)
+
+
+@asynccontextmanager
+async def lifespan(_: FastAPI) -> AsyncIterator[None]:
+    backend = settings.cache_backend
+    if backend == 'in-memory':
+        logger.info('Using in-memory backend for caching')
+        FastAPICache.init(InMemoryBackend(),
+                          prefix="fastapi-cache",
+                          key_builder=valis_cache_key_builder)
+    elif backend == 'redis':
+        logger.info('Using Redis backend for caching')
+        redis = RedisAsync.from_url("redis://localhost")
+        FastAPICache.init(RedisBackend(redis),
+                          prefix="fastapi-cache",
+                          key_builder=valis_cache_key_builder)
+    elif backend == 'null' or not backend:
+        logger.info('Using null backend for caching')
+        FastAPICache.init(NullCacheBackend(),
+                          prefix="fastapi-cache",
+                          key_builder=valis_cache_key_builder)
+    else:
+        raise ValueError(f'Invalid cache backend {backend}')
+
+    yield
+
+
+async def valis_cache_key_builder(
+    func,
+    namespace: str = "",
+    request: Request | None = None,
+    _: Response | None = None,
+    *args,
+    **kwargs,
+):
+    query_params = request.query_params.items() if request else []
+
+    try:
+        body_json = await request.json()
+        body = sorted(body_json.items()) if body_json else []
+    except json.JSONDecodeError:
+        body = []
+
+    hash = hashlib.new('md5')
+    for param,value in list(query_params) + body:
+        hash.update(param.encode())
+        hash.update(str(value).encode())
+
+    params_hash = hash.hexdigest()[0:8]
+
+    url = request.url.path.replace('/', '_') if request else ""
+    if url.startswith('_'):
+        url = url[1:]
+
+    chunks = [
+            namespace,
+            request.method.lower() if request else "",
+            url,
+            params_hash,
+        ]
+
+    return ":".join(chunks)
+
+
+def valis_cache(
+    expire: Optional[int] = settings.cache_ttl,
+    coder: Optional[Type[Coder]] = ORJsonCoder,
+    key_builder: Optional[KeyBuilder] = None,
+    namespace: str = "valis-cache",
+    injected_dependency_namespace: str = "__fastapi_cache",
+) -> Callable[[Callable[P, Awaitable[R]]], Callable[P, Awaitable[Union[R, Response]]]]:
+    """Caches an API route.
+
+    This is a copy of the ``cache`` decorator from ``fastapi_cache`` with some
+    modifications to allow using it with POST requests. This version should be used
+    with a key builder that hashes the body of the request in addition to the function
+    arguments.
+
+    The main change is that the call to ``fastapi_cache.decorator._uncacheable`` has
+    been removed and we accept all route types. `.valis_cache_key_builder` looks
+    at the body of the request and hashes its body so that POST requests to the same
+    route with different parameters are cached separately. It also defaults to
+    ``settings.cache_ttl`` for the expiration time of the cached value.
+
+    """
+
+    injected_request = Parameter(
+        name=f"{injected_dependency_namespace}_request",
+        annotation=Request,
+        kind=Parameter.KEYWORD_ONLY,
+    )
+    injected_response = Parameter(
+        name=f"{injected_dependency_namespace}_response",
+        annotation=Response,
+        kind=Parameter.KEYWORD_ONLY,
+    )
+
+    def wrapper(
+        func: Callable[P, Awaitable[R]]
+    ) -> Callable[P, Awaitable[Union[R, Response]]]:
+        # get_typed_signature ensures that any forward references are resolved first
+        wrapped_signature = get_typed_signature(func)
+        to_inject: List[Parameter] = []
+        request_param = _locate_param(wrapped_signature, injected_request, to_inject)
+        response_param = _locate_param(wrapped_signature, injected_response, to_inject)
+        return_type = get_typed_return_annotation(func)
+
+        @wraps(func)
+        async def inner(*args: P.args, **kwargs: P.kwargs) -> Union[R, Response]:
+            nonlocal coder
+            nonlocal expire
+            nonlocal key_builder
+
+            async def ensure_async_func(*args: P.args, **kwargs: P.kwargs) -> R:
+                """Run cached sync functions in thread pool just like FastAPI."""
+                # if the wrapped function does NOT have request or response in
+                # its function signature, make sure we don't pass them in as
+                # keyword arguments
+                kwargs.pop(injected_request.name, None)
+                kwargs.pop(injected_response.name, None)
+
+                if iscoroutinefunction(func):
+                    # async, return as is.
+                    # unintuitively, we have to await once here, so that caller
+                    # does not have to await twice. See
+                    # https://stackoverflow.com/a/59268198/532513
+                    return await func(*args, **kwargs)
+                else:
+                    # sync, wrap in thread and return async
+                    # see above why we have to await even although caller also awaits.
+                    return await run_in_threadpool(func, *args, **kwargs)  # type: ignore[arg-type]
+
+            copy_kwargs = kwargs.copy()
+            request: Optional[Request] = copy_kwargs.pop(request_param.name, None)  # type: ignore[assignment]
+            response: Optional[Response] = copy_kwargs.pop(response_param.name, None)  # type: ignore[assignment]
+
+            prefix = FastAPICache.get_prefix()
+            coder = coder or FastAPICache.get_coder()
+            expire = expire or FastAPICache.get_expire()
+            key_builder = key_builder or FastAPICache.get_key_builder()
+            backend = FastAPICache.get_backend()
+            cache_status_header = FastAPICache.get_cache_status_header()
+
+            cache_key = key_builder(
+                func,
+                f"{prefix}:{namespace}",
+                request=request,
+                response=response,
+                args=args,
+                kwargs=copy_kwargs,
+            )
+            if isawaitable(cache_key):
+                cache_key = await cache_key
+            assert isinstance(cache_key, str)  # noqa: S101  # assertion is a type guard
+
+            try:
+                ttl, cached = await backend.get_with_ttl(cache_key)
+            except Exception:
+                logger.warning(
+                    f"Error retrieving cache key '{cache_key}' from backend:",
+                    exc_info=True,
+                )
+                ttl, cached = 0, None
+
+            if cached is None  or (request is not None and request.headers.get("Cache-Control") == "no-cache"):  # cache miss
+                result = await ensure_async_func(*args, **kwargs)
+                to_cache = coder.encode(result)
+
+                try:
+                    await backend.set(cache_key, to_cache, expire)
+                except Exception:
+                    logger.warning(
+                        f"Error setting cache key '{cache_key}' in backend:",
+                        exc_info=True,
+                    )
+
+                if response:
+                    response.headers.update(
+                        {
+                            "Cache-Control": f"max-age={expire}",
+                            "ETag": f"W/{hash(to_cache)}",
+                            cache_status_header: "MISS",
+                        }
+                    )
+
+            else:  # cache hit
+                if response:
+                    etag = f"W/{hash(cached)}"
+                    response.headers.update(
+                        {
+                            "Cache-Control": f"max-age={ttl}",
+                            "ETag": etag,
+                            cache_status_header: "HIT",
+                        }
+                    )
+
+                    if_none_match = request and request.headers.get("if-none-match")
+                    if if_none_match == etag:
+                        response.status_code = HTTP_304_NOT_MODIFIED
+                        return response
+
+                result = cast(R, coder.decode_as_type(cached, type_=return_type))
+
+            return result
+
+        inner.__signature__ = _augment_signature(wrapped_signature, *to_inject)  # type: ignore[attr-defined]
+
+        return inner
+
+    return wrapper
+
+
+class NullCacheBackend(Backend):
+    """A null cache backend that does no caching and always runs the route."""
+
+    async def get_with_ttl(self, key: str) -> Tuple[int, Optional[bytes]]:
+        return 0, None
+
+    async def get(self, key: str) -> Optional[bytes]:
+        return None
+
+    async def set(self, key: str, value: bytes, expire: Optional[int] = None) -> None:
+        pass
+
+    async def clear(self, namespace: Optional[str] = None, key: Optional[str] = None) -> int:
+        pass
+
+
+def clear_redis_cache(namespace: Optional[str] = None,
+                      host: str = 'localhost',
+                      port: int = 6379) -> None:
+    """Clears the Redis cache.
+
+    Parameters
+    ----------
+    namespace
+        The namespace to clear, e.g., ``valis-target``. If ``None``, all the
+        ``valis-*`` keys under the ``fastapi-cache`` namespace will be cleared.
+    host
+        The Redis host.
+    port
+        The Redis port.
+
+    """
+
+    redis = Redis.from_url(f"redis://{host}:{port}")
+
+    if namespace is None:
+        # There is no good way in Redis to delete an entire namespace so we need
+        # to get all the keys and delete them one by one.
+        keys = redis.keys("fastapi-cache:valis-*")
+        namespaces: set[str] = set()
+        for key in keys:
+            valis_namespace = re.match(rb"fastapi-cache:(valis-\w+):", key)
+            if valis_namespace:
+                namespaces.add(valis_namespace.group(1).decode())
+
+    else:
+        namespaces = {namespace}
+
+    for namespace in namespaces:
+        # Same here. For each namespace we get its keys and delete them.
+        namespace_keys = redis.keys(f"fastapi-cache:{namespace}:*")
+        for key in namespace_keys:
+            redis.delete(key)