From d7ba2620070e0d3befb736d1bd9aebc6acdc2d96 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 13 Mar 2024 16:03:38 -0400 Subject: [PATCH 1/3] chore: update base image and dependencies --- Dockerfile | 4 +- dev.Dockerfile | 4 +- poetry.lock | 674 +++++++++++++++++++++++++------------------------ pyproject.toml | 2 +- 4 files changed, 344 insertions(+), 340 deletions(-) diff --git a/Dockerfile b/Dockerfile index f5c68c0..29b9cc4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,8 +1,8 @@ -FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.02.01 +FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.03.01 # Use uvicorn (instead of hypercorn) in production since I've found # multiple benchmarks showing it to be faster - David L -RUN pip install --no-cache-dir "uvicorn[standard]==0.27.1" +RUN pip install --no-cache-dir "uvicorn[standard]==0.28.0" # Backwards-compatible with old BentoV2 container layout WORKDIR /service-registry diff --git a/dev.Dockerfile b/dev.Dockerfile index 2e8790c..7649580 100644 --- a/dev.Dockerfile +++ b/dev.Dockerfile @@ -1,6 +1,6 @@ -FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.02.01 +FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.03.01 -RUN pip install --no-cache-dir "uvicorn[standard]==0.27.1" +RUN pip install --no-cache-dir "uvicorn[standard]==0.28.0" # Backwards-compatible with old BentoV2 container layout WORKDIR /service-registry diff --git a/poetry.lock b/poetry.lock index 01cfbaa..0b3e4a0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.1 and should not be changed by hand. [[package]] name = "aiodns" @@ -148,13 +148,13 @@ files = [ [[package]] name = "anyio" -version = "4.2.0" +version = "4.3.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.8" files = [ - {file = "anyio-4.2.0-py3-none-any.whl", hash = "sha256:745843b39e829e108e518c489b31dc757de7d2131d53fac32bd8df268227bfee"}, - {file = "anyio-4.2.0.tar.gz", hash = "sha256:e1875bb4b4e2de1669f4bc7869b6d3f54231cdced71605e6e64c9be77e3be50f"}, + {file = "anyio-4.3.0-py3-none-any.whl", hash = "sha256:048e05d0f6caeed70d731f3db756d35dcc1f35747c8c403364a8332c630441b8"}, + {file = "anyio-4.3.0.tar.gz", hash = "sha256:f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6"}, ] [package.dependencies] @@ -200,19 +200,19 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p [[package]] name = "bento-lib" -version = "11.5.0" +version = "11.5.1" description = "A set of common utilities and helpers for Bento platform services." optional = false python-versions = ">=3.10,<4.0" files = [ - {file = "bento_lib-11.5.0-py3-none-any.whl", hash = "sha256:aedbc3665980724d92b93a59642cae545b0d1f280f838878f0cbb16d4dc9fc78"}, - {file = "bento_lib-11.5.0.tar.gz", hash = "sha256:e609b352c494cf6c96f45ef0080bb69bf97ad46a134d35104daa4287ea815a00"}, + {file = "bento_lib-11.5.1-py3-none-any.whl", hash = "sha256:5dfd48a15158dcaa0c0c90f1fd37d60b1a6f7d8fb157780eacc9c7d438a22b33"}, + {file = "bento_lib-11.5.1.tar.gz", hash = "sha256:3b77b292c49a66aa8e9463d550cd38c4d355fbb9863ff598f9084a3ccc7eac77"}, ] [package.dependencies] aiofiles = ">=23.2.1,<24.0.0" aiohttp = ">=3.9.3,<4" -fastapi = {version = ">=0.104,<0.110", optional = true, markers = "extra == \"fastapi\""} +fastapi = {version = ">=0.104,<0.111", optional = true, markers = "extra == \"fastapi\""} jsonschema = ">=4.20.0,<5" psycopg2-binary = ">=2.9.9,<3.0" pydantic = ">=2.5.2,<3" @@ -224,18 +224,18 @@ werkzeug = ">=2.2.3,<4" 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"sha256:4238949c5ffe6876362d9c0180fc6c3a824a7b12b80604eeb8085f2ed7460de3"}, - {file = "virtualenv-20.25.0.tar.gz", hash = "sha256:bf51c0d9c7dd63ea8e44086fa1e4fb1093a31e963b86959257378aef020e1f1b"}, + {file = "virtualenv-20.25.1-py3-none-any.whl", hash = "sha256:961c026ac520bac5f69acb8ea063e8a4f071bcc9457b9c1f28f6b085c511583a"}, + {file = "virtualenv-20.25.1.tar.gz", hash = "sha256:e08e13ecdca7a0bd53798f356d5831434afa5b07b93f0abdf0797b7a06ffe197"}, ] [package.dependencies] diff --git a/pyproject.toml b/pyproject.toml index 464e418..d165834 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api" [tool.poetry] name = "bento_service_registry" -version = "1.3.5" +version = "1.3.6" description = "An implementation of GA4GH Service Registry API for the Bento platform." authors = ["David Lougheed "] readme = "README.md" From 3238eb751634b888aba2b013e1ad0ac994e9c03f Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 13 Mar 2024 16:04:07 -0400 Subject: [PATCH 2/3] chore: log time taken to fetch workflows --- bento_service_registry/workflows.py | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/bento_service_registry/workflows.py b/bento_service_registry/workflows.py index 2f48a0a..70d5579 100644 --- a/bento_service_registry/workflows.py +++ b/bento_service_registry/workflows.py @@ -2,6 +2,7 @@ import asyncio import logging +from datetime import datetime from fastapi import Depends, status from typing import Annotated from urllib.parse import urljoin @@ -26,6 +27,7 @@ async def get_workflows_from_service( http_session: aiohttp.ClientSession, logger: logging.Logger, service: dict, + start_dt: datetime, ) -> WorkflowsByPurpose: service_url: str | None = service.get("url") @@ -34,16 +36,23 @@ async def get_workflows_from_service( return {} service_url_norm: str = service_url.rstrip("/") + "/" + workflows_url: str = urljoin(service_url_norm, "workflows") + + async with http_session.get(workflows_url, headers=authz_header) as res: + data = await res.json() + time_taken = (datetime.now() - start_dt).total_seconds() - async with http_session.get(urljoin(service_url_norm, "workflows"), headers=authz_header) as res: if res.status != status.HTTP_200_OK: logger.error( - f"Got non-200 response from data type service ({service_url=}): {res.status=}; body={await res.json()}") + f"Got non-200 response from data type service ({service_url=}): {res.status=}; body={data}; " + f"took {time_taken:.1f}s") return {} + logger.info(f"{workflows_url}: took {time_taken:.1f}s") + wfs: dict[str, dict[str, dict]] = {} - for purpose, purpose_wfs in (await res.json()).items(): + for purpose, purpose_wfs in data.items(): if purpose not in wfs: wfs[purpose] = {} # TODO: pydantic model + validation @@ -67,8 +76,9 @@ async def get_workflows( logger.debug(f"Found {len(workflow_services)} workflow-providing services") + start_dt = datetime.now() service_wfs = await asyncio.gather( - *(get_workflows_from_service(authz_header, http_session, logger, s) for s in workflow_services) + *(get_workflows_from_service(authz_header, http_session, logger, s, start_dt) for s in workflow_services) ) workflows_from_services: WorkflowsByPurpose = {} From f410041aae8b9f9f9369d046decb04efa8e9e6f8 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 13 Mar 2024 16:17:49 -0400 Subject: [PATCH 3/3] chore: change some info logs to debug logs --- bento_service_registry/services.py | 2 +- bento_service_registry/workflows.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/bento_service_registry/services.py b/bento_service_registry/services.py index 10972d1..7a66e62 100644 --- a/bento_service_registry/services.py +++ b/bento_service_registry/services.py @@ -70,7 +70,7 @@ async def get_service( try: service_resp = {**(await r.json()), "url": s_url} - self._logger.info(f"{service_info_url}: Took {(datetime.now() - dt).total_seconds():.1f}s") + self._logger.debug(f"{service_info_url}: Took {(datetime.now() - dt).total_seconds():.1f}s") except (JSONDecodeError, aiohttp.ContentTypeError, TypeError) as e: # JSONDecodeError can happen if the JSON is invalid # ContentTypeError can happen if the Content-Type is not application/json diff --git a/bento_service_registry/workflows.py b/bento_service_registry/workflows.py index 70d5579..8e5b4ea 100644 --- a/bento_service_registry/workflows.py +++ b/bento_service_registry/workflows.py @@ -48,7 +48,7 @@ async def get_workflows_from_service( f"took {time_taken:.1f}s") return {} - logger.info(f"{workflows_url}: took {time_taken:.1f}s") + logger.debug(f"{workflows_url}: took {time_taken:.1f}s") wfs: dict[str, dict[str, dict]] = {} @@ -80,6 +80,7 @@ async def get_workflows( service_wfs = await asyncio.gather( *(get_workflows_from_service(authz_header, http_session, logger, s, start_dt) for s in workflow_services) ) + logger.debug(f"Fetching all workflows took {(datetime.now() - start_dt).total_seconds():.1f}s") workflows_from_services: WorkflowsByPurpose = {} workflows_found: int = 0