From 179490c6abea1d20d6ec7981e1e20866b93e8f51 Mon Sep 17 00:00:00 2001 From: Faisal Alquaddoomi Date: Mon, 2 Oct 2023 11:11:20 -0600 Subject: [PATCH] Extracts Oak from API server into a standalone RPC server (#357) ### Related issues - Relates to #347 ### Summary - adds RPC server to expose Oak's compare() method - adds [wait-for-it.sh](https://github.com/vishnubob/wait-for-it), a simple and often-used script for polling a TCP service until it's ready (used to check when the RPC server is up) - changes API from running via uvicorn to running via gunicorn, but with the uvicorn worker class - fixes high memory usage and some transient concurrency issues when the number of API workers is increased ### Notes - I was briefly trying to make better use of Docker layer caching and, in the process, switched the references to poetry in `start_api.sh` from full paths to just `poetry`. It appeared to work fine, so I didn't switch them back, but if there's a reason to use those full paths by all means feel free to reintroduce them. ### Checks - [ ] All tests have passed (or issues created for failing tests) --- backend/poetry.lock | 171 ++++++++++++++++++++- backend/pyproject.toml | 2 + backend/src/monarch_py/api/config.py | 31 +++- backend/src/monarch_py/api/oak_server.py | 46 ++++++ backend/start_api.sh | 16 +- backend/wait-for-it.sh | 183 +++++++++++++++++++++++ 6 files changed, 443 insertions(+), 6 deletions(-) create mode 100644 backend/src/monarch_py/api/oak_server.py create mode 100755 backend/wait-for-it.sh diff --git a/backend/poetry.lock b/backend/poetry.lock index 147a62fa4..4a493b1a2 100644 --- a/backend/poetry.lock +++ b/backend/poetry.lock @@ -860,6 +860,26 @@ files = [ [package.dependencies] colorama = ">=0.4" +[[package]] +name = "gunicorn" +version = "21.2.0" +description = "WSGI HTTP Server for UNIX" +optional = false +python-versions = ">=3.5" 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"705e768052ec47326fbe0159829008e14701b91d31863d00ad152bacd10efd9b" diff --git a/backend/pyproject.toml b/backend/pyproject.toml index 3172b0d58..b056c6a24 100644 --- a/backend/pyproject.toml +++ b/backend/pyproject.toml @@ -30,6 +30,8 @@ pystow = ">=0.5.0" loguru = "*" fastapi = "^0.103.1" oaklib = "^0.5.19" +gunicorn = "^21.2.0" +tinyrpc = {extras = ["zmq"], version = "^1.1.7"} [tool.poetry.group.dev.dependencies] diff --git a/backend/src/monarch_py/api/config.py b/backend/src/monarch_py/api/config.py index 763c5848b..8bc760d9f 100644 --- a/backend/src/monarch_py/api/config.py +++ b/backend/src/monarch_py/api/config.py @@ -1,10 +1,17 @@ import os +import zmq from functools import lru_cache from pydantic import BaseSettings +from tinyrpc import RPCClient +from tinyrpc.protocols.jsonrpc import JSONRPCProtocol +from tinyrpc.transports.zmq import ZmqClientTransport + from monarch_py.implementations.oak.oak_implementation import OakImplementation from monarch_py.implementations.solr.solr_implementation import SolrImplementation +from monarch_py.datamodels.model import TermSetPairwiseSimilarity + class Settings(BaseSettings): @@ -13,6 +20,8 @@ class Settings(BaseSettings): solr_url = os.getenv("SOLR_URL") if os.getenv("SOLR_URL") else f"http://{solr_host}:{solr_port}/solr" phenio_db_path = os.getenv("PHENIO_DB_PATH") if os.getenv("PHENIO_DB_PATH") else "/data/phenio.db" + oak_server_host = os.getenv("OAK_SERVER_HOST", '127.0.0.1') + oak_server_port = os.getenv("OAK_SERVER_PORT", 18811) settings = Settings() @@ -21,8 +30,26 @@ class Settings(BaseSettings): def solr(): return SolrImplementation(settings.solr_url) +class OakRPCMarshaller: + def __init__(self) -> None: + ctx = zmq.Context() + rpc_client = RPCClient( + JSONRPCProtocol(), + ZmqClientTransport.create( + ctx, f'tcp://{settings.oak_server_host}:{settings.oak_server_port}' + ) + ) + self.oak_server = rpc_client.get_proxy() + + def compare(self, *args, **kwargs): + # for some reason TermSetPairwiseSimilarity is not JSON-serializable so + # we can't call compare() directly. instead, we call compare_as_dict(), + # which sends back a dict, and then we convert it into the expected + # TermSetPairwiseSimilarity type + result = self.oak_server.compare_as_dict(*args, **kwargs) + return TermSetPairwiseSimilarity(**result) + @lru_cache(maxsize=1) def oak(): - phenio_db_path = settings.phenio_db_path if os.path.exists(settings.phenio_db_path) else None - return OakImplementation().init_semsim(phenio_path=phenio_db_path) + return OakRPCMarshaller() diff --git a/backend/src/monarch_py/api/oak_server.py b/backend/src/monarch_py/api/oak_server.py new file mode 100644 index 000000000..1d3112b69 --- /dev/null +++ b/backend/src/monarch_py/api/oak_server.py @@ -0,0 +1,46 @@ +import os +from typing import List + +import zmq + +from tinyrpc.server import RPCServer +from tinyrpc.dispatch import RPCDispatcher +from tinyrpc.protocols.jsonrpc import JSONRPCProtocol +from tinyrpc.transports.zmq import ZmqServerTransport + +from monarch_py.implementations.oak.oak_implementation import OakImplementation +# from monarch_py.datamodels.model import TermSetPairwiseSimilarity +from monarch_py.api.config import settings + +def run_server(): + # first load oak, before starting the server + phenio_db_path = settings.phenio_db_path if os.path.exists(settings.phenio_db_path) else None + oak = OakImplementation().init_semsim(phenio_path=phenio_db_path) + + # set up all the bits that a tinyrpc server is made of + ctx = zmq.Context() + dispatcher = RPCDispatcher() + transport = ZmqServerTransport.create( + ctx, f'tcp://{settings.oak_server_host}:{settings.oak_server_port}' + ) + + rpc_server = RPCServer( + transport, + JSONRPCProtocol(), + dispatcher + ) + + # register a serializable proxy for the compare method + @dispatcher.public + def compare_as_dict( + subjects: List[str], objects: List[str], predicates: List[str] = None, labels=False + ) -> dict: + return oak.compare( + subjects=subjects, objects=objects, + predicates=predicates, labels=labels + ).dict() + + rpc_server.serve_forever() + +if __name__ == '__main__': + run_server() diff --git a/backend/start_api.sh b/backend/start_api.sh index d462f5b38..b78a3fc9a 100755 --- a/backend/start_api.sh +++ b/backend/start_api.sh @@ -1,7 +1,17 @@ #!/usr/bin/bash -# check for uvicorn workers env var, default to 1 -UVICORN_WORKERS=${UVICORN_WORKERS:-1} +# before we start, run the oak server in the background... +poetry run python -m src.monarch_py.api.oak_server & + +# ...but block while we wait for it to start serving request +./wait-for-it.sh -t 0 ${OAK_SERVER_HOST:-localhost}:${OAK_SERVER_PORT:-18811} + +# check for uvicorn workers env var, default to 8 +UVICORN_WORKERS=${UVICORN_WORKERS:-8} # Start the API -/opt/poetry/bin/poetry run uvicorn src.monarch_py.api.main:app --host 0.0.0.0 --port 8000 --workers ${UVICORN_WORKERS} +poetry run gunicorn src.monarch_py.api.main:app \ + --bind 0.0.0.0:8000 \ + --preload --timeout ${WORKER_TIMEOUT:-120} \ + --worker-class uvicorn.workers.UvicornWorker \ + --workers ${UVICORN_WORKERS} diff --git a/backend/wait-for-it.sh b/backend/wait-for-it.sh new file mode 100755 index 000000000..a0ea5275e --- /dev/null +++ b/backend/wait-for-it.sh @@ -0,0 +1,183 @@ +#!/usr/bin/env bash +# from https://github.com/vishnubob/wait-for-it/blob/81b1373f17855a4dc21156cfe1694c31d7d1792e/wait-for-it.sh +# Use this script to test if a given TCP host/port are available + +WAITFORIT_cmdname=${0##*/} + +echoerr() { if [[ $WAITFORIT_QUIET -ne 1 ]]; then echo "$@" 1>&2; fi } + +usage() +{ + cat << USAGE >&2 +Usage: + $WAITFORIT_cmdname host:port [-s] [-t timeout] [-- command args] + -h HOST | --host=HOST Host or IP under test + -p PORT | --port=PORT TCP port under test + Alternatively, you specify the host and port as host:port + -s | --strict Only execute subcommand if the test succeeds + -q | --quiet Don't output any status messages + -t TIMEOUT | --timeout=TIMEOUT + Timeout in seconds, zero for no timeout + -- COMMAND ARGS Execute command with args after the test finishes +USAGE + exit 1 +} + +wait_for() +{ + if [[ $WAITFORIT_TIMEOUT -gt 0 ]]; then + echoerr "$WAITFORIT_cmdname: waiting $WAITFORIT_TIMEOUT seconds for $WAITFORIT_HOST:$WAITFORIT_PORT" + else + echoerr "$WAITFORIT_cmdname: waiting for $WAITFORIT_HOST:$WAITFORIT_PORT without a timeout" + fi + WAITFORIT_start_ts=$(date +%s) + while : + do + if [[ $WAITFORIT_ISBUSY -eq 1 ]]; then + nc -z $WAITFORIT_HOST $WAITFORIT_PORT + WAITFORIT_result=$? + else + (echo -n > /dev/tcp/$WAITFORIT_HOST/$WAITFORIT_PORT) >/dev/null 2>&1 + WAITFORIT_result=$? + fi + if [[ $WAITFORIT_result -eq 0 ]]; then + WAITFORIT_end_ts=$(date +%s) + echoerr "$WAITFORIT_cmdname: $WAITFORIT_HOST:$WAITFORIT_PORT is available after $((WAITFORIT_end_ts - WAITFORIT_start_ts)) seconds" + break + fi + sleep 1 + done + return $WAITFORIT_result +} + +wait_for_wrapper() +{ + # In order to support SIGINT during timeout: http://unix.stackexchange.com/a/57692 + if [[ $WAITFORIT_QUIET -eq 1 ]]; then + timeout $WAITFORIT_BUSYTIMEFLAG $WAITFORIT_TIMEOUT $0 --quiet --child --host=$WAITFORIT_HOST --port=$WAITFORIT_PORT --timeout=$WAITFORIT_TIMEOUT & + else + timeout $WAITFORIT_BUSYTIMEFLAG $WAITFORIT_TIMEOUT $0 --child --host=$WAITFORIT_HOST --port=$WAITFORIT_PORT --timeout=$WAITFORIT_TIMEOUT & + fi + WAITFORIT_PID=$! + trap "kill -INT -$WAITFORIT_PID" INT + wait $WAITFORIT_PID + WAITFORIT_RESULT=$? + if [[ $WAITFORIT_RESULT -ne 0 ]]; then + echoerr "$WAITFORIT_cmdname: timeout occurred after waiting $WAITFORIT_TIMEOUT seconds for $WAITFORIT_HOST:$WAITFORIT_PORT" + fi + return $WAITFORIT_RESULT +} + +# process arguments +while [[ $# -gt 0 ]] +do + case "$1" in + *:* ) + WAITFORIT_hostport=(${1//:/ }) + WAITFORIT_HOST=${WAITFORIT_hostport[0]} + WAITFORIT_PORT=${WAITFORIT_hostport[1]} + shift 1 + ;; + --child) + WAITFORIT_CHILD=1 + shift 1 + ;; + -q | --quiet) + WAITFORIT_QUIET=1 + shift 1 + ;; + -s | --strict) + WAITFORIT_STRICT=1 + shift 1 + ;; + -h) + WAITFORIT_HOST="$2" + if [[ $WAITFORIT_HOST == "" ]]; then break; fi + shift 2 + ;; + --host=*) + WAITFORIT_HOST="${1#*=}" + shift 1 + ;; + -p) + WAITFORIT_PORT="$2" + if [[ $WAITFORIT_PORT == "" ]]; then break; fi + shift 2 + ;; + --port=*) + WAITFORIT_PORT="${1#*=}" + shift 1 + ;; + -t) + WAITFORIT_TIMEOUT="$2" + if [[ $WAITFORIT_TIMEOUT == "" ]]; then break; fi + shift 2 + ;; + --timeout=*) + WAITFORIT_TIMEOUT="${1#*=}" + shift 1 + ;; + --) + shift + WAITFORIT_CLI=("$@") + break + ;; + --help) + usage + ;; + *) + echoerr "Unknown argument: $1" + usage + ;; + esac +done + +if [[ "$WAITFORIT_HOST" == "" || "$WAITFORIT_PORT" == "" ]]; then + echoerr "Error: you need to provide a host and port to test." + usage +fi + +WAITFORIT_TIMEOUT=${WAITFORIT_TIMEOUT:-15} +WAITFORIT_STRICT=${WAITFORIT_STRICT:-0} +WAITFORIT_CHILD=${WAITFORIT_CHILD:-0} +WAITFORIT_QUIET=${WAITFORIT_QUIET:-0} + +# Check to see if timeout is from busybox? +WAITFORIT_TIMEOUT_PATH=$(type -p timeout) +WAITFORIT_TIMEOUT_PATH=$(realpath $WAITFORIT_TIMEOUT_PATH 2>/dev/null || readlink -f $WAITFORIT_TIMEOUT_PATH) + +WAITFORIT_BUSYTIMEFLAG="" +if [[ $WAITFORIT_TIMEOUT_PATH =~ "busybox" ]]; then + WAITFORIT_ISBUSY=1 + # Check if busybox timeout uses -t flag + # (recent Alpine versions don't support -t anymore) + if timeout &>/dev/stdout | grep -q -e '-t '; then + WAITFORIT_BUSYTIMEFLAG="-t" + fi +else + WAITFORIT_ISBUSY=0 +fi + +if [[ $WAITFORIT_CHILD -gt 0 ]]; then + wait_for + WAITFORIT_RESULT=$? + exit $WAITFORIT_RESULT +else + if [[ $WAITFORIT_TIMEOUT -gt 0 ]]; then + wait_for_wrapper + WAITFORIT_RESULT=$? + else + wait_for + WAITFORIT_RESULT=$? + fi +fi + +if [[ $WAITFORIT_CLI != "" ]]; then + if [[ $WAITFORIT_RESULT -ne 0 && $WAITFORIT_STRICT -eq 1 ]]; then + echoerr "$WAITFORIT_cmdname: strict mode, refusing to execute subprocess" + exit $WAITFORIT_RESULT + fi + exec "${WAITFORIT_CLI[@]}" +else + exit $WAITFORIT_RESULT +fi