From 0ff3d5f7ec606c8d78b64b663c6b2b7d9819dbdd Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Sat, 7 Jan 2023 15:06:02 -0500 Subject: [PATCH 01/20] chore!: work on new chord_services format with support for external services (public, beacon) --- bento_service_registry/app.py | 2 +- bento_service_registry/routes.py | 5 +++-- bento_service_registry/types.py | 20 ++++++++++++++++++++ pyproject.toml | 2 +- tests/chord_services.json | 21 +++++---------------- 5 files changed, 30 insertions(+), 20 deletions(-) create mode 100644 bento_service_registry/types.py diff --git a/bento_service_registry/app.py b/bento_service_registry/app.py index 18396de..51b7f8b 100644 --- a/bento_service_registry/app.py +++ b/bento_service_registry/app.py @@ -31,7 +31,7 @@ def create_app(): app.config.from_mapping( BENTO_DEBUG=get_bento_debug(), BENTO_VALIDATE_SSL=not get_bento_debug(), - CHORD_SERVICES=os.environ.get("CHORD_SERVICES", os.environ.get("BENTO_SERVICES", "chord_services.json")), + BENTO_SERVICES=os.environ.get("CHORD_SERVICES", os.environ.get("BENTO_SERVICES", "chord_services.json")), CHORD_URL=os.environ.get("CHORD_URL", os.environ.get("BENTO_URL", "http://0.0.0.0:5000/")), # Own node's URL CONTACT_TIMEOUT=int(os.environ.get("CONTACT_TIMEOUT", 5)), SERVICE_ID=os.environ.get("SERVICE_ID", ":".join(SERVICE_TYPE.values())), diff --git a/bento_service_registry/routes.py b/bento_service_registry/routes.py index 37b2118..f565856 100644 --- a/bento_service_registry/routes.py +++ b/bento_service_registry/routes.py @@ -28,8 +28,9 @@ async def get_chord_services() -> list[dict]: Reads the list of services from the chord_services.json file """ try: - async with aiofiles.open(current_app.config["CHORD_SERVICES"], "r") as f: - return [s for s in json.loads(await f.read()) if not s.get("disabled")] # Skip disabled services + async with aiofiles.open(current_app.config["BENTO_SERVICES"], "r") as f: + # Return dictionary of services (id: configuration) Skip disabled services + return {sk: sv for sk, sv in json.loads(await f.read()).items() if not sv.get("disabled")} except Exception as e: except_name = type(e).__name__ print("Error retrieving information from chord_services JSON file:", except_name) diff --git a/bento_service_registry/types.py b/bento_service_registry/types.py new file mode 100644 index 0000000..3e6927f --- /dev/null +++ b/bento_service_registry/types.py @@ -0,0 +1,20 @@ +from __future__ import annotations + +from typing import TypedDict + + +# TODO: py3.10(?): optional TypedDict props + +# required props for chord_services.json entries +class BaseBentoService(TypedDict): + url_template: str + repository: str + data_service: bool + + +# optional props for chord_services.json entries +class BentoService(BaseBentoService, total=False): + manageable_tables: bool + + +BentoServices = dict[str, BentoService] diff --git a/pyproject.toml b/pyproject.toml index b65ad14..922cd59 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api" [tool.poetry] name = "bento_service_registry" -version = "0.8.0" +version = "0.9.0" description = "An implementation of GA4GH Service Registry API for the Bento platform." authors = ["David Lougheed "] readme = "README.md" diff --git a/tests/chord_services.json b/tests/chord_services.json index 1b266a5..b995dde 100644 --- a/tests/chord_services.json +++ b/tests/chord_services.json @@ -1,18 +1,7 @@ -[ - { - "type": { - "organization": "ca.c3g.bento", - "artifact": "service-registry", - "language": "python" - }, +{ + "service-registry": { + "url_template": "{BENTO_URL}api/{id}", "repository": "https://github.com/bento-platform/bento_service_registry", - "data_service": false, - "wsgi": true, - "python_module": "bento_service_registry.app", - "python_callable": "application", - "run_environment": { - "CHORD_SERVICES": "./tests/chord_services.json", - "URL_PATH_FORMAT": "" - } + "data_service": false } -] +} From c6860efa6057ea40ab5dd113bad97e28bdd245c7 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Sat, 7 Jan 2023 15:58:24 -0500 Subject: [PATCH 02/20] start working on new chord_services schema --- bento_service_registry/app.py | 5 ++++- bento_service_registry/routes.py | 30 +++++++++++++++++++++++------- bento_service_registry/types.py | 3 +++ tests/chord_services.json | 3 ++- 4 files changed, 32 insertions(+), 9 deletions(-) diff --git a/bento_service_registry/app.py b/bento_service_registry/app.py index 51b7f8b..84ba048 100644 --- a/bento_service_registry/app.py +++ b/bento_service_registry/app.py @@ -28,11 +28,14 @@ def get_bento_debug(): def create_app(): app = Quart(__name__) + bento_url = os.environ.get("CHORD_URL", os.environ.get("BENTO_URL", "http://0.0.0.0:5000/")) # Own node's URL app.config.from_mapping( BENTO_DEBUG=get_bento_debug(), BENTO_VALIDATE_SSL=not get_bento_debug(), BENTO_SERVICES=os.environ.get("CHORD_SERVICES", os.environ.get("BENTO_SERVICES", "chord_services.json")), - CHORD_URL=os.environ.get("CHORD_URL", os.environ.get("BENTO_URL", "http://0.0.0.0:5000/")), # Own node's URL + BENTO_URL=bento_url, + BENTO_PUBLIC_URL=os.environ.get("BENTO_PUBLIC_URL", bento_url), + BENTO_PORTAL_PUBLIC_URL=os.environ.get("BENTO_PORTAL_PUBLIC_URL", bento_url), CONTACT_TIMEOUT=int(os.environ.get("CONTACT_TIMEOUT", 5)), SERVICE_ID=os.environ.get("SERVICE_ID", ":".join(SERVICE_TYPE.values())), URL_PATH_FORMAT=os.environ.get("URL_PATH_FORMAT", "api/{artifact}"), diff --git a/bento_service_registry/routes.py b/bento_service_registry/routes.py index f565856..5570ac2 100644 --- a/bento_service_registry/routes.py +++ b/bento_service_registry/routes.py @@ -15,26 +15,42 @@ from urllib.parse import urljoin from .constants import SERVICE_NAME, SERVICE_TYPE, SERVICE_ARTIFACT +from .types import BentoService service_registry = Blueprint("service_registry", __name__) -def get_service_url(artifact: str) -> str: - return urljoin(current_app.config["CHORD_URL"], current_app.config["URL_PATH_FORMAT"].format(artifact=artifact)) - - -async def get_chord_services() -> list[dict]: +async def get_chord_services() -> dict[str, dict]: """ Reads the list of services from the chord_services.json file """ try: async with aiofiles.open(current_app.config["BENTO_SERVICES"], "r") as f: # Return dictionary of services (id: configuration) Skip disabled services - return {sk: sv for sk, sv in json.loads(await f.read()).items() if not sv.get("disabled")} + chord_services_data: dict[str, BentoService] = json.loads(await f.read()) + return { + sk: { + **sv, + "url": sv["url_template"].format( + BENTO_URL=current_app.config["BENTO_URL"], + BENTO_PUBLIC_URL=current_app.config["BENTO_PUBLIC_URL"], + BENTO_PORTAL_PUBLIC_URL=current_app.config["BENTO_PORTAL_PUBLIC_URL"], + **sv, + ), + } + for sk, sv in chord_services_data.items() + if not sv.get("disabled") + } + except Exception as e: except_name = type(e).__name__ print("Error retrieving information from chord_services JSON file:", except_name) - return [] + return {} + + +def get_service_url(artifact: str) -> str: + chord_services_by_artifact = {sv["artifact"]: sv for sv in (await get_chord_services()).values()} + return chord_services_by_artifact[artifact]["url"] async def get_service(session: aiohttp.ClientSession, service_artifact: str) -> Optional[dict[str, dict]]: diff --git a/bento_service_registry/types.py b/bento_service_registry/types.py index 3e6927f..c6d96be 100644 --- a/bento_service_registry/types.py +++ b/bento_service_registry/types.py @@ -14,7 +14,10 @@ class BaseBentoService(TypedDict): # optional props for chord_services.json entries class BentoService(BaseBentoService, total=False): + artifact: str + url: str manageable_tables: bool + disabled: bool BentoServices = dict[str, BentoService] diff --git a/tests/chord_services.json b/tests/chord_services.json index b995dde..8d7a515 100644 --- a/tests/chord_services.json +++ b/tests/chord_services.json @@ -1,6 +1,7 @@ { "service-registry": { - "url_template": "{BENTO_URL}api/{id}", + "artifact": "service-registry", + "url_template": "{BENTO_URL}api/{artifact}", "repository": "https://github.com/bento-platform/bento_service_registry", "data_service": false } From d4f6aa5f7f861b1172518ca19b11c24bc5e97028 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Sat, 7 Jan 2023 16:16:50 -0500 Subject: [PATCH 03/20] fix async stuff --- bento_service_registry/routes.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bento_service_registry/routes.py b/bento_service_registry/routes.py index 5570ac2..b287b9e 100644 --- a/bento_service_registry/routes.py +++ b/bento_service_registry/routes.py @@ -48,7 +48,7 @@ async def get_chord_services() -> dict[str, dict]: return {} -def get_service_url(artifact: str) -> str: +async def get_service_url(artifact: str) -> str: chord_services_by_artifact = {sv["artifact"]: sv for sv in (await get_chord_services()).values()} return chord_services_by_artifact[artifact]["url"] @@ -60,7 +60,7 @@ async def get_service(session: aiohttp.ClientSession, service_artifact: str) -> timeout = aiohttp.ClientTimeout(total=current_app.config["CONTACT_TIMEOUT"]) - s_url: str = get_service_url(service_artifact) + s_url: str = await get_service_url(service_artifact) service_info_url: str = urljoin(f"{s_url}/", "service-info") # Optional Authorization HTTP header to forward to nested requests @@ -161,7 +161,7 @@ async def get_service_info() -> GA4GHServiceInfo: }, "contactUrl": "mailto:info@c3g.ca", "version": __version__, - "url": get_service_url(SERVICE_ARTIFACT), + "url": await get_service_url(SERVICE_ARTIFACT), "environment": "prod" } From fe9f934e67679d4de6b6cf64fb1c5ba36a657d8d Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Sat, 7 Jan 2023 16:32:48 -0500 Subject: [PATCH 04/20] fix issue with making service-info list + typing issues --- bento_service_registry/routes.py | 47 ++++++++++++++++++++------------ 1 file changed, 29 insertions(+), 18 deletions(-) diff --git a/bento_service_registry/routes.py b/bento_service_registry/routes.py index b287b9e..ede098a 100644 --- a/bento_service_registry/routes.py +++ b/bento_service_registry/routes.py @@ -5,13 +5,14 @@ import asyncio import sys -from bento_lib.responses.quart_errors import quart_not_found_error +import quart +from bento_lib.responses.quart_errors import quart_not_found_error, quart_internal_server_error from bento_lib.types import GA4GHServiceInfo from bento_service_registry import __version__ from datetime import datetime from json.decoder import JSONDecodeError from quart import Blueprint, current_app, json, request -from typing import Optional +from typing import Optional, Union from urllib.parse import urljoin from .constants import SERVICE_NAME, SERVICE_TYPE, SERVICE_ARTIFACT @@ -20,7 +21,7 @@ service_registry = Blueprint("service_registry", __name__) -async def get_chord_services() -> dict[str, dict]: +async def get_chord_services() -> dict[str, BentoService]: """ Reads the list of services from the chord_services.json file """ @@ -29,15 +30,15 @@ async def get_chord_services() -> dict[str, dict]: # Return dictionary of services (id: configuration) Skip disabled services chord_services_data: dict[str, BentoService] = json.loads(await f.read()) return { - sk: { + sk: BentoService( **sv, - "url": sv["url_template"].format( + url=sv["url_template"].format( BENTO_URL=current_app.config["BENTO_URL"], BENTO_PUBLIC_URL=current_app.config["BENTO_PUBLIC_URL"], BENTO_PORTAL_PUBLIC_URL=current_app.config["BENTO_PORTAL_PUBLIC_URL"], **sv, ), - } + ) # type: ignore for sk, sv in chord_services_data.items() if not sv.get("disabled") } @@ -53,14 +54,16 @@ async def get_service_url(artifact: str) -> str: return chord_services_by_artifact[artifact]["url"] -async def get_service(session: aiohttp.ClientSession, service_artifact: str) -> Optional[dict[str, dict]]: +async def get_service(session: aiohttp.ClientSession, service_metadata: BentoService) -> Optional[dict[str, dict]]: + artifact = service_metadata["artifact"] + # special case: requesting info about the current service. Skip networking / self-connect. - if service_artifact == SERVICE_ARTIFACT: + if artifact == SERVICE_ARTIFACT: return await get_service_info() timeout = aiohttp.ClientTimeout(total=current_app.config["CONTACT_TIMEOUT"]) - s_url: str = await get_service_url(service_artifact) + s_url: str = service_metadata["url"] service_info_url: str = urljoin(f"{s_url}/", "service-info") # Optional Authorization HTTP header to forward to nested requests @@ -77,7 +80,7 @@ async def get_service(session: aiohttp.ClientSession, service_artifact: str) -> async with session.get(service_info_url, headers=headers, timeout=timeout) as r: if r.status != 200: r_text = await r.text() - print(f"[{SERVICE_NAME}] Non-200 status code on {service_artifact}: {r.status}\n" + print(f"[{SERVICE_NAME}] Non-200 status code on {artifact}: {r.status}\n" f" Content: {r_text}", file=sys.stderr, flush=True) # If we have the special case where we got a JWT error from the proxy script, we can safely print out @@ -89,7 +92,7 @@ async def get_service(session: aiohttp.ClientSession, service_artifact: str) -> return None try: - service_resp[service_artifact] = {**(await r.json()), "url": s_url} + service_resp[artifact] = {**(await r.json()), "url": s_url} except JSONDecodeError: print(f"[{SERVICE_NAME}] Encountered invalid response from {service_info_url}: {await r.text()}") @@ -102,7 +105,7 @@ async def get_service(session: aiohttp.ClientSession, service_artifact: str) -> print(f"[{SERVICE_NAME}] Encountered connection error with {service_info_url}: {str(e)}", file=sys.stderr, flush=True) - return service_resp.get(service_artifact) + return service_resp.get(artifact) @service_registry.route("/bento-services") @@ -116,8 +119,8 @@ async def get_services() -> list[dict]: connector=aiohttp.TCPConnector(ssl=current_app.config["BENTO_VALIDATE_SSL"])) as session: # noinspection PyTypeChecker service_list: list[Optional[dict]] = await asyncio.gather(*[ - get_service(session, s["type"]["artifact"]) - for s in (await get_chord_services()) + get_service(session, s) + for s in (await get_chord_services()).values() ]) return [s for s in service_list if s is not None] @@ -128,18 +131,26 @@ async def services(): @service_registry.route("/services/") -async def service_by_id(service_id: str): +async def service_by_id(service_id: str) -> Union[quart.Response, dict]: services_by_id = {s["id"]: s for s in (await get_services())} + chord_services_by_artifact = await get_chord_services() + if service_id not in services_by_id: return quart_not_found_error(f"Service with ID {service_id} was not found in registry") async with aiohttp.ClientSession( connector=aiohttp.TCPConnector(ssl=current_app.config["BENTO_VALIDATE_SSL"])) as session: - return await get_service(session, services_by_id[service_id]["type"]["artifact"]) + service_data = await get_service( + session, chord_services_by_artifact[services_by_id[service_id]["type"]["artifact"]]) + + if service_data is None: + return quart_internal_server_error(f"An internal error was encountered with service with ID {service_id}") + + return service_data @service_registry.route("/services/types") -async def service_types(): +async def service_types() -> quart.Response: types_by_key: dict[str, dict] = {} for st in (s["type"] for s in await get_services()): sk = ":".join(st.values()) @@ -197,6 +208,6 @@ async def get_service_info() -> GA4GHServiceInfo: @service_registry.route("/service-info") -async def service_info(): +async def service_info() -> quart.Response: # Spec: https://github.com/ga4gh-discovery/ga4gh-service-info return json.jsonify(await get_service_info()) From ae14851ff7bb1fdefb5b61dde715d5a395b48a90 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Sat, 7 Jan 2023 16:35:08 -0500 Subject: [PATCH 05/20] future annotations --- tests/conftest.py | 2 ++ tests/test_api.py | 2 ++ 2 files changed, 4 insertions(+) diff --git a/tests/conftest.py b/tests/conftest.py index 130125d..58368f9 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,3 +1,5 @@ +from __future__ import annotations + import aiohttp import os import pytest diff --git a/tests/test_api.py b/tests/test_api.py index f5cbddc..764a2d1 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -1,3 +1,5 @@ +from __future__ import annotations + import pytest from bento_service_registry.app import get_bento_debug From 9716fc15a5bce17e611002ab0ee11ae97c247073 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Sat, 7 Jan 2023 16:43:05 -0500 Subject: [PATCH 06/20] use old typehinting for mypy --- bento_service_registry/app.py | 2 -- bento_service_registry/constants.py | 2 -- bento_service_registry/routes.py | 14 ++++++-------- bento_service_registry/types.py | 2 -- tests/conftest.py | 2 -- tests/test_api.py | 2 -- 6 files changed, 6 insertions(+), 18 deletions(-) diff --git a/bento_service_registry/app.py b/bento_service_registry/app.py index 84ba048..8b31e99 100644 --- a/bento_service_registry/app.py +++ b/bento_service_registry/app.py @@ -1,5 +1,3 @@ -from __future__ import annotations - import os import subprocess import sys diff --git a/bento_service_registry/constants.py b/bento_service_registry/constants.py index 98ac5a1..67bf440 100644 --- a/bento_service_registry/constants.py +++ b/bento_service_registry/constants.py @@ -1,5 +1,3 @@ -from __future__ import annotations - from bento_lib.types import GA4GHServiceType from bento_service_registry import __version__ diff --git a/bento_service_registry/routes.py b/bento_service_registry/routes.py index ede098a..82d6dc7 100644 --- a/bento_service_registry/routes.py +++ b/bento_service_registry/routes.py @@ -1,5 +1,3 @@ -from __future__ import annotations - import aiofiles import aiohttp import asyncio @@ -12,7 +10,7 @@ from datetime import datetime from json.decoder import JSONDecodeError from quart import Blueprint, current_app, json, request -from typing import Optional, Union +from typing import Dict, Optional, Union from urllib.parse import urljoin from .constants import SERVICE_NAME, SERVICE_TYPE, SERVICE_ARTIFACT @@ -21,14 +19,14 @@ service_registry = Blueprint("service_registry", __name__) -async def get_chord_services() -> dict[str, BentoService]: +async def get_chord_services() -> Dict[str, BentoService]: """ Reads the list of services from the chord_services.json file """ try: async with aiofiles.open(current_app.config["BENTO_SERVICES"], "r") as f: # Return dictionary of services (id: configuration) Skip disabled services - chord_services_data: dict[str, BentoService] = json.loads(await f.read()) + chord_services_data: Dict[str, BentoService] = json.loads(await f.read()) return { sk: BentoService( **sv, @@ -54,7 +52,7 @@ async def get_service_url(artifact: str) -> str: return chord_services_by_artifact[artifact]["url"] -async def get_service(session: aiohttp.ClientSession, service_metadata: BentoService) -> Optional[dict[str, dict]]: +async def get_service(session: aiohttp.ClientSession, service_metadata: BentoService) -> Optional[Dict[str, dict]]: artifact = service_metadata["artifact"] # special case: requesting info about the current service. Skip networking / self-connect. @@ -74,7 +72,7 @@ async def get_service(session: aiohttp.ClientSession, service_metadata: BentoSer dt = datetime.now() print(f"[{SERVICE_NAME}] Contacting {service_info_url}{' with bearer token' if auth_header else ''}", flush=True) - service_resp: dict[str, dict] = {} + service_resp: Dict[str, dict] = {} try: async with session.get(service_info_url, headers=headers, timeout=timeout) as r: @@ -151,7 +149,7 @@ async def service_by_id(service_id: str) -> Union[quart.Response, dict]: @service_registry.route("/services/types") async def service_types() -> quart.Response: - types_by_key: dict[str, dict] = {} + types_by_key: Dict[str, dict] = {} for st in (s["type"] for s in await get_services()): sk = ":".join(st.values()) types_by_key[sk] = st diff --git a/bento_service_registry/types.py b/bento_service_registry/types.py index c6d96be..2c32809 100644 --- a/bento_service_registry/types.py +++ b/bento_service_registry/types.py @@ -1,5 +1,3 @@ -from __future__ import annotations - from typing import TypedDict diff --git a/tests/conftest.py b/tests/conftest.py index 58368f9..130125d 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,5 +1,3 @@ -from __future__ import annotations - import aiohttp import os import pytest diff --git a/tests/test_api.py b/tests/test_api.py index 764a2d1..f5cbddc 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -1,5 +1,3 @@ -from __future__ import annotations - import pytest from bento_service_registry.app import get_bento_debug From 17061c58a918417b73bdbbd790b1e85be72dadd7 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Sat, 7 Jan 2023 16:48:45 -0500 Subject: [PATCH 07/20] more revert --- bento_service_registry/routes.py | 6 +++--- bento_service_registry/types.py | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/bento_service_registry/routes.py b/bento_service_registry/routes.py index 82d6dc7..64092aa 100644 --- a/bento_service_registry/routes.py +++ b/bento_service_registry/routes.py @@ -10,7 +10,7 @@ from datetime import datetime from json.decoder import JSONDecodeError from quart import Blueprint, current_app, json, request -from typing import Dict, Optional, Union +from typing import Dict, List, Optional, Union from urllib.parse import urljoin from .constants import SERVICE_NAME, SERVICE_TYPE, SERVICE_ARTIFACT @@ -112,11 +112,11 @@ async def chord_services(): return json.jsonify(await get_chord_services()) -async def get_services() -> list[dict]: +async def get_services() -> List[dict]: async with aiohttp.ClientSession( connector=aiohttp.TCPConnector(ssl=current_app.config["BENTO_VALIDATE_SSL"])) as session: # noinspection PyTypeChecker - service_list: list[Optional[dict]] = await asyncio.gather(*[ + service_list: List[Optional[dict]] = await asyncio.gather(*[ get_service(session, s) for s in (await get_chord_services()).values() ]) diff --git a/bento_service_registry/types.py b/bento_service_registry/types.py index 2c32809..e7b743d 100644 --- a/bento_service_registry/types.py +++ b/bento_service_registry/types.py @@ -18,4 +18,4 @@ class BentoService(BaseBentoService, total=False): disabled: bool -BentoServices = dict[str, BentoService] +BentoServices = Dict[str, BentoService] From 7437a038da18383832745ed4add20053eaca74ff Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Sat, 7 Jan 2023 17:03:17 -0500 Subject: [PATCH 08/20] oops --- bento_service_registry/types.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bento_service_registry/types.py b/bento_service_registry/types.py index e7b743d..656dd01 100644 --- a/bento_service_registry/types.py +++ b/bento_service_registry/types.py @@ -1,4 +1,4 @@ -from typing import TypedDict +from typing import Dict, TypedDict # TODO: py3.10(?): optional TypedDict props From ae9a0a65e189234a62735d1b699173bf35ad4736 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Sat, 7 Jan 2023 17:31:32 -0500 Subject: [PATCH 09/20] catch less extraneous stuff --- bento_service_registry/app.py | 1 - bento_service_registry/routes.py | 34 ++++++++++++++++++-------------- 2 files changed, 19 insertions(+), 16 deletions(-) diff --git a/bento_service_registry/app.py b/bento_service_registry/app.py index 8b31e99..fee797c 100644 --- a/bento_service_registry/app.py +++ b/bento_service_registry/app.py @@ -36,7 +36,6 @@ def create_app(): BENTO_PORTAL_PUBLIC_URL=os.environ.get("BENTO_PORTAL_PUBLIC_URL", bento_url), CONTACT_TIMEOUT=int(os.environ.get("CONTACT_TIMEOUT", 5)), SERVICE_ID=os.environ.get("SERVICE_ID", ":".join(SERVICE_TYPE.values())), - URL_PATH_FORMAT=os.environ.get("URL_PATH_FORMAT", "api/{artifact}"), ) path_for_git = os.path.abspath(os.path.join(os.path.dirname(__file__), "..")) diff --git a/bento_service_registry/routes.py b/bento_service_registry/routes.py index 64092aa..45bc16f 100644 --- a/bento_service_registry/routes.py +++ b/bento_service_registry/routes.py @@ -23,29 +23,33 @@ async def get_chord_services() -> Dict[str, BentoService]: """ Reads the list of services from the chord_services.json file """ + + # Load bento_services.json data from the filesystem try: async with aiofiles.open(current_app.config["BENTO_SERVICES"], "r") as f: # Return dictionary of services (id: configuration) Skip disabled services chord_services_data: Dict[str, BentoService] = json.loads(await f.read()) - return { - sk: BentoService( - **sv, - url=sv["url_template"].format( - BENTO_URL=current_app.config["BENTO_URL"], - BENTO_PUBLIC_URL=current_app.config["BENTO_PUBLIC_URL"], - BENTO_PORTAL_PUBLIC_URL=current_app.config["BENTO_PORTAL_PUBLIC_URL"], - **sv, - ), - ) # type: ignore - for sk, sv in chord_services_data.items() - if not sv.get("disabled") - } - except Exception as e: except_name = type(e).__name__ - print("Error retrieving information from chord_services JSON file:", except_name) + print("Error retrieving information from chord_services JSON file:", except_name, file=sys.stderr) return {} + return { + sk: BentoService( + **sv, + url=sv["url_template"].format( + BENTO_URL=current_app.config["BENTO_URL"], + BENTO_PUBLIC_URL=current_app.config["BENTO_PUBLIC_URL"], + BENTO_PORTAL_PUBLIC_URL=current_app.config["BENTO_PORTAL_PUBLIC_URL"], + **sv, + ), + ) # type: ignore + for sk, sv in chord_services_data.items() + if not sv.get("disabled") + } + + + async def get_service_url(artifact: str) -> str: chord_services_by_artifact = {sv["artifact"]: sv for sv in (await get_chord_services()).values()} From 7c5dff20c032d82424f103d8f7b2c77e1aa914b5 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Sat, 7 Jan 2023 17:35:44 -0500 Subject: [PATCH 10/20] remove whitespace --- bento_service_registry/routes.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/bento_service_registry/routes.py b/bento_service_registry/routes.py index 45bc16f..2390853 100644 --- a/bento_service_registry/routes.py +++ b/bento_service_registry/routes.py @@ -49,8 +49,6 @@ async def get_chord_services() -> Dict[str, BentoService]: } - - async def get_service_url(artifact: str) -> str: chord_services_by_artifact = {sv["artifact"]: sv for sv in (await get_chord_services()).values()} return chord_services_by_artifact[artifact]["url"] From 2bfa3ae19f1e057b0e7ee691971e62751a971521 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 9 Jan 2023 11:27:34 -0500 Subject: [PATCH 11/20] fix: handle aiohttp content type err --- bento_service_registry/routes.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bento_service_registry/routes.py b/bento_service_registry/routes.py index 2390853..636dda5 100644 --- a/bento_service_registry/routes.py +++ b/bento_service_registry/routes.py @@ -93,7 +93,7 @@ async def get_service(session: aiohttp.ClientSession, service_metadata: BentoSer try: service_resp[artifact] = {**(await r.json()), "url": s_url} - except JSONDecodeError: + except (JSONDecodeError, aiohttp.ContentTypeError): print(f"[{SERVICE_NAME}] Encountered invalid response from {service_info_url}: {await r.text()}") print(f"[{SERVICE_NAME}] {service_info_url}: Took {(datetime.now() - dt).total_seconds():.1f}s", flush=True) From 8b225e5877c0088662fe260197353938b019bbc7 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 9 Jan 2023 11:28:23 -0500 Subject: [PATCH 12/20] chore: more in depth log for invalid response errors --- bento_service_registry/routes.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/bento_service_registry/routes.py b/bento_service_registry/routes.py index 636dda5..df10da7 100644 --- a/bento_service_registry/routes.py +++ b/bento_service_registry/routes.py @@ -93,8 +93,9 @@ async def get_service(session: aiohttp.ClientSession, service_metadata: BentoSer try: service_resp[artifact] = {**(await r.json()), "url": s_url} - except (JSONDecodeError, aiohttp.ContentTypeError): - print(f"[{SERVICE_NAME}] Encountered invalid response from {service_info_url}: {await r.text()}") + except (JSONDecodeError, aiohttp.ContentTypeError) as e: + print(f"[{SERVICE_NAME}] Encountered invalid response ({str(e)}) from {service_info_url}: " + f"{await r.text()}") print(f"[{SERVICE_NAME}] {service_info_url}: Took {(datetime.now() - dt).total_seconds():.1f}s", flush=True) From ed4b94f7e74f598e70a1b69832d34f0e680da069 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Fri, 13 Jan 2023 10:34:04 -0500 Subject: [PATCH 13/20] feat: validate ssl flag --- bento_service_registry/app.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/bento_service_registry/app.py b/bento_service_registry/app.py index fee797c..df44647 100644 --- a/bento_service_registry/app.py +++ b/bento_service_registry/app.py @@ -16,20 +16,26 @@ from .constants import SERVICE_TYPE, SERVICE_NAME from .routes import service_registry +TRUTH_VALUES = ("true", "1") + def get_bento_debug(): # This is a function to allow monkey-patching the environment on app startup. return os.environ.get( "CHORD_DEBUG", os.environ.get("BENTO_DEBUG", os.environ.get("QUART_ENV", "production")) - ).strip().lower() in ("true", "1", "development") + ).strip().lower() in (*TRUTH_VALUES, "development") def create_app(): app = Quart(__name__) bento_url = os.environ.get("CHORD_URL", os.environ.get("BENTO_URL", "http://0.0.0.0:5000/")) # Own node's URL + + bento_debug = get_bento_debug() + validate_ssl = os.environ.get("BENTO_VALIDATE_SSL", str(not bento_debug)).strip().lower() in TRUTH_VALUES + app.config.from_mapping( - BENTO_DEBUG=get_bento_debug(), - BENTO_VALIDATE_SSL=not get_bento_debug(), + BENTO_DEBUG=bento_debug, + BENTO_VALIDATE_SSL=validate_ssl, BENTO_SERVICES=os.environ.get("CHORD_SERVICES", os.environ.get("BENTO_SERVICES", "chord_services.json")), BENTO_URL=bento_url, BENTO_PUBLIC_URL=os.environ.get("BENTO_PUBLIC_URL", bento_url), From 11f0a2e8073fc3643a3ba284e066dd94452c9f2f Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Fri, 13 Jan 2023 10:35:25 -0500 Subject: [PATCH 14/20] chore: update 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version="^5.0.2", extras = ["quart"] } +bento-lib = {extras = ["quart"], version = "^5.2.0"} [tool.poetry.group.dev.dependencies] codecov = "^2.1.12" From 3e8deb49de07680bf244e82f96899fe34bfa9e03 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Fri, 13 Jan 2023 10:35:41 -0500 Subject: [PATCH 15/20] feat: add bento service kind support --- bento_service_registry/constants.py | 2 ++ bento_service_registry/routes.py | 47 ++++++++++++++++++----------- bento_service_registry/types.py | 2 +- 3 files changed, 33 insertions(+), 18 deletions(-) diff --git a/bento_service_registry/constants.py b/bento_service_registry/constants.py index 67bf440..6c85564 100644 --- a/bento_service_registry/constants.py +++ b/bento_service_registry/constants.py @@ -2,11 +2,13 @@ from bento_service_registry import __version__ __all__ = [ + "BENTO_SERVICE_KIND", "SERVICE_ARTIFACT", "SERVICE_TYPE", "SERVICE_NAME", ] +BENTO_SERVICE_KIND: str = "service-registry" SERVICE_ARTIFACT: str = "service-registry" # For exact implementations, this should be org.ga4gh/service-registry/1.0.0. diff --git a/bento_service_registry/routes.py b/bento_service_registry/routes.py index df10da7..b3ffa5f 100644 --- a/bento_service_registry/routes.py +++ b/bento_service_registry/routes.py @@ -13,13 +13,13 @@ from typing import Dict, List, Optional, Union from urllib.parse import urljoin -from .constants import SERVICE_NAME, SERVICE_TYPE, SERVICE_ARTIFACT +from .constants import BENTO_SERVICE_KIND, SERVICE_NAME, SERVICE_TYPE, SERVICE_ARTIFACT from .types import BentoService service_registry = Blueprint("service_registry", __name__) -async def get_chord_services() -> Dict[str, BentoService]: +async def get_chord_services_by_compose_id() -> Dict[str, BentoService]: """ Reads the list of services from the chord_services.json file """ @@ -49,16 +49,19 @@ async def get_chord_services() -> Dict[str, BentoService]: } -async def get_service_url(artifact: str) -> str: - chord_services_by_artifact = {sv["artifact"]: sv for sv in (await get_chord_services()).values()} - return chord_services_by_artifact[artifact]["url"] +async def get_chord_services_by_kind() -> Dict[str, BentoService]: + return {sv["service_kind"]: sv for sv in (await get_chord_services_by_compose_id()).values()} + + +async def get_service_url(service_kind: str) -> str: + return (await get_chord_services_by_kind())[service_kind]["url"] async def get_service(session: aiohttp.ClientSession, service_metadata: BentoService) -> Optional[Dict[str, dict]]: - artifact = service_metadata["artifact"] + kind = service_metadata["service_kind"] # special case: requesting info about the current service. Skip networking / self-connect. - if artifact == SERVICE_ARTIFACT: + if kind == BENTO_SERVICE_KIND: return await get_service_info() timeout = aiohttp.ClientTimeout(total=current_app.config["CONTACT_TIMEOUT"]) @@ -80,7 +83,7 @@ async def get_service(session: aiohttp.ClientSession, service_metadata: BentoSer async with session.get(service_info_url, headers=headers, timeout=timeout) as r: if r.status != 200: r_text = await r.text() - print(f"[{SERVICE_NAME}] Non-200 status code on {artifact}: {r.status}\n" + print(f"[{SERVICE_NAME}] Non-200 status code on {kind}: {r.status}\n" f" Content: {r_text}", file=sys.stderr, flush=True) # If we have the special case where we got a JWT error from the proxy script, we can safely print out @@ -92,7 +95,7 @@ async def get_service(session: aiohttp.ClientSession, service_metadata: BentoSer return None try: - service_resp[artifact] = {**(await r.json()), "url": s_url} + service_resp[kind] = {**(await r.json()), "url": s_url} except (JSONDecodeError, aiohttp.ContentTypeError) as e: print(f"[{SERVICE_NAME}] Encountered invalid response ({str(e)}) from {service_info_url}: " f"{await r.text()}") @@ -106,13 +109,13 @@ async def get_service(session: aiohttp.ClientSession, service_metadata: BentoSer print(f"[{SERVICE_NAME}] Encountered connection error with {service_info_url}: {str(e)}", file=sys.stderr, flush=True) - return service_resp.get(artifact) + return service_resp.get(kind) @service_registry.route("/bento-services") @service_registry.route("/chord-services") async def chord_services(): - return json.jsonify(await get_chord_services()) + return json.jsonify(await get_chord_services_by_compose_id()) async def get_services() -> List[dict]: @@ -121,7 +124,7 @@ async def get_services() -> List[dict]: # noinspection PyTypeChecker service_list: List[Optional[dict]] = await asyncio.gather(*[ get_service(session, s) - for s in (await get_chord_services()).values() + for s in (await get_chord_services_by_compose_id()).values() ]) return [s for s in service_list if s is not None] @@ -134,15 +137,18 @@ async def services(): @service_registry.route("/services/") async def service_by_id(service_id: str) -> Union[quart.Response, dict]: services_by_id = {s["id"]: s for s in (await get_services())} - chord_services_by_artifact = await get_chord_services() + chord_services_by_kind = await get_chord_services_by_kind() if service_id not in services_by_id: return quart_not_found_error(f"Service with ID {service_id} was not found in registry") + svc = services_by_id[service_id] + async with aiohttp.ClientSession( connector=aiohttp.TCPConnector(ssl=current_app.config["BENTO_VALIDATE_SSL"])) as session: + # Get service by bento.serviceKind, using type.artifact as a backup for legacy reasons service_data = await get_service( - session, chord_services_by_artifact[services_by_id[service_id]["type"]["artifact"]]) + session, chord_services_by_kind[svc.get("bento", {}).get("serviceKind", svc["type"]["artifact"])]) if service_data is None: return quart_internal_server_error(f"An internal error was encountered with service with ID {service_id}") @@ -174,7 +180,10 @@ async def get_service_info() -> GA4GHServiceInfo: "contactUrl": "mailto:info@c3g.ca", "version": __version__, "url": await get_service_url(SERVICE_ARTIFACT), - "environment": "prod" + "environment": "prod", + "bento": { + "serviceKind": BENTO_SERVICE_KIND, + }, } if not current_app.config["BENTO_DEBUG"]: @@ -190,7 +199,9 @@ async def get_service_info() -> GA4GHServiceInfo: ) res_tag, _ = await git_proc.communicate() if res_tag: - service_info_dict["git_tag"] = res_tag.decode().rstrip() + res_tag_str: str = res_tag.decode().rstrip() + service_info_dict["git_tag"] = res_tag_str + service_info_dict["bento"]["gitTag"] = res_tag_str git_proc = await asyncio.create_subprocess_exec( "git", "branch", "--show-current", @@ -199,7 +210,9 @@ async def get_service_info() -> GA4GHServiceInfo: ) res_branch, _ = await git_proc.communicate() if res_branch: - service_info_dict["git_branch"] = res_branch.decode().rstrip() + res_branch_str: str = res_branch.decode().rstrip() + service_info_dict["git_branch"] = res_branch_str + service_info_dict["bento"]["gitBranch"] = res_branch_str except Exception as e: except_name = type(e).__name__ diff --git a/bento_service_registry/types.py b/bento_service_registry/types.py index 656dd01..88ab421 100644 --- a/bento_service_registry/types.py +++ b/bento_service_registry/types.py @@ -12,7 +12,7 @@ class BaseBentoService(TypedDict): # optional props for chord_services.json entries class BentoService(BaseBentoService, total=False): - artifact: str + service_kind: str url: str manageable_tables: bool disabled: bool From d0d22e6002adf1aafc7672c03f4bf67ac9206c97 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Fri, 13 Jan 2023 11:21:39 -0500 Subject: [PATCH 16/20] fix: test --- tests/chord_services.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/chord_services.json b/tests/chord_services.json index 8d7a515..8c2e0e9 100644 --- a/tests/chord_services.json +++ b/tests/chord_services.json @@ -1,7 +1,7 @@ { "service-registry": { - "artifact": "service-registry", - "url_template": "{BENTO_URL}api/{artifact}", + "service_kind": "service-registry", + "url_template": "{BENTO_URL}api/{service_kind}", "repository": "https://github.com/bento-platform/bento_service_registry", "data_service": false } From bdba5e22bc5c3ac435dc05a710c3083246691bf8 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 7 Feb 2023 17:09:14 -0500 Subject: [PATCH 17/20] chore: update dependencies --- poetry.lock | 362 +++++++++++++++++++++++++------------------------ pyproject.toml | 2 +- 2 files changed, 187 insertions(+), 177 deletions(-) diff --git a/poetry.lock b/poetry.lock index 8f68ec1..107fde3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -184,14 +184,14 @@ tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy [[package]] name = "bento-lib" -version = "5.2.0" +version = "5.4.0" description = "A set of common utilities and helpers for Bento platform services." category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "bento_lib-5.2.0-py3-none-any.whl", hash = "sha256:b8a84cbd4d0dd150ed187ddb93ea05fb7e36f6554be3fa09f6d8dca9309dbb72"}, - {file = "bento_lib-5.2.0.tar.gz", hash = "sha256:c2dec47bdb56caee982c1d526f3926cc98818a923b5d9c8d6a90d3a0e202e28d"}, + {file = "bento_lib-5.4.0-py3-none-any.whl", hash = "sha256:4bba8fa2a8510d16dcec6800354096a218b1320858175b0e90719af85f584a13"}, + {file = "bento_lib-5.4.0.tar.gz", hash = "sha256:db21a35d5135ad58ad1cb49c4c66b0637d500d52ee188ed5db0df1fdc09b0727"}, ] [package.dependencies] @@ -222,14 +222,14 @@ files = [ [[package]] name = "cachetools" -version = "5.2.0" +version = "5.3.0" description = "Extensible memoizing collections and decorators" category = "dev" optional = false python-versions = "~=3.7" files = [ - {file = "cachetools-5.2.0-py3-none-any.whl", hash 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hash = "sha256:b1d5eb14f221506f50d6604a561f4c5786d9e80355219694a1b244bcd96f4567"}, + {file = "platformdirs-3.0.0.tar.gz", hash = "sha256:8a1228abb1ef82d788f74139988b137e78692984ec7b08eaa6c65f1723af28f9"}, ] [package.extras] -docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.5)"] -test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"] +docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)"] +test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"] [[package]] name = "pluggy" @@ -1286,14 +1296,14 @@ files = [ [[package]] name = "pyproject-api" -version = "1.4.0" +version = "1.5.0" description = "API to interact with the python pyproject.toml based projects" category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "pyproject_api-1.4.0-py3-none-any.whl", hash = "sha256:c34226297781efdd1ba4dfb74ce21076d9a8360e2125ea31803c1a02c76b2460"}, - {file = "pyproject_api-1.4.0.tar.gz", hash = "sha256:ac85c1f82e0291dbae5a7739dbb9a990e11ee4034c9b5599ea714f07a24ecd71"}, + {file = "pyproject_api-1.5.0-py3-none-any.whl", hash = "sha256:4c111277dfb96bcd562c6245428f27250b794bfe3e210b8714c4f893952f2c17"}, + {file = "pyproject_api-1.5.0.tar.gz", hash = "sha256:0962df21f3e633b8ddb9567c011e6c1b3dcdfc31b7860c0ede7e24c5a1200fbe"}, ] [package.dependencies] @@ -1343,14 +1353,14 @@ files = [ [[package]] name = "pytest" -version = "7.2.0" +version = "7.2.1" description = "pytest: simple powerful testing with Python" category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "pytest-7.2.0-py3-none-any.whl", hash = "sha256:892f933d339f068883b6fd5a459f03d85bfcb355e4981e146d2c7616c21fef71"}, - {file = "pytest-7.2.0.tar.gz", hash = "sha256:c4014eb40e10f11f355ad4e3c2fb2c6c6d1919c73f3b5a433de4708202cade59"}, + {file = "pytest-7.2.1-py3-none-any.whl", hash = "sha256:c7c6ca206e93355074ae32f7403e8ea12163b1163c976fee7d4d84027c162be5"}, + {file = "pytest-7.2.1.tar.gz", hash = "sha256:d45e0952f3727241918b8fd0f376f5ff6b301cc0777c6f9a556935c92d8a7d42"}, ] [package.dependencies] @@ -1447,19 +1457,19 @@ hiredis = ["hiredis (>=0.1.3)"] [[package]] name = "requests" -version = "2.28.1" +version = "2.28.2" description = "Python HTTP for Humans." category = "main" optional = false python-versions = ">=3.7, <4" files = [ - {file = "requests-2.28.1-py3-none-any.whl", hash = "sha256:8fefa2a1a1365bf5520aac41836fbee479da67864514bdb821f31ce07ce65349"}, - {file = "requests-2.28.1.tar.gz", hash = "sha256:7c5599b102feddaa661c826c56ab4fee28bfd17f5abca1ebbe3e7f19d7c97983"}, + {file = "requests-2.28.2-py3-none-any.whl", hash = "sha256:64299f4909223da747622c030b781c0d7811e359c37124b4bd368fb8c6518baa"}, + {file = "requests-2.28.2.tar.gz", hash = "sha256:98b1b2782e3c6c4904938b84c0eb932721069dfdb9134313beff7c83c2df24bf"}, ] [package.dependencies] certifi = ">=2017.4.17" -charset-normalizer = ">=2,<3" +charset-normalizer = ">=2,<4" idna = ">=2.5,<4" urllib3 = ">=1.21.1,<1.27" @@ -1493,42 +1503,42 @@ files = [ [[package]] name = "tox" -version = "4.2.5" +version = "4.4.4" description = "tox is a generic virtualenv management and test command line tool" category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "tox-4.2.5-py3-none-any.whl", hash = "sha256:a256447ec85a058004231f19ca3df66b3be591a7561c8f8389d1d60b5b629989"}, - {file = "tox-4.2.5.tar.gz", hash = "sha256:dba263a7da1151e3f7c0816bf9efcbad127ee7ec981e5f03b9666b47619c735e"}, + {file = "tox-4.4.4-py3-none-any.whl", hash = "sha256:1195820ca35b141ce5ab040c9dfad8f03de6897c9bd867c6151dfb7dc58e64cd"}, + {file = "tox-4.4.4.tar.gz", hash = "sha256:e1ef01d9e9503b1218511f74517dc3f0008c8b5e0cc53ab7f51ff3c2ca63b349"}, ] [package.dependencies] -cachetools = ">=5.2" +cachetools = ">=5.2.1" chardet = ">=5.1" colorama = ">=0.4.6" filelock = ">=3.9" -packaging = ">=22" +packaging = ">=23" platformdirs = ">=2.6.2" pluggy = ">=1" -pyproject-api = ">=1.2.1" +pyproject-api = ">=1.5" tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""} virtualenv = ">=20.17.1" [package.extras] -docs = ["furo (>=2022.12.7)", "sphinx (>=6)", "sphinx-argparse-cli (>=1.10)", "sphinx-autodoc-typehints (>=1.19.5)", "sphinx-copybutton (>=0.5.1)", "sphinx-inline-tabs (>=2022.1.2b11)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"] -testing = ["build[virtualenv] (>=0.9)", "covdefaults (>=2.2.2)", "devpi-process (>=0.3)", "diff-cover (>=7.3)", "distlib (>=0.3.6)", "flaky (>=3.7)", "hatch-vcs (>=0.3)", "hatchling (>=1.12)", "psutil (>=5.9.4)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest-xdist (>=3.1)", "re-assert (>=1.1)", "time-machine (>=2.8.2)"] +docs = ["furo (>=2022.12.7)", "sphinx (>=6.1.3)", "sphinx-argparse-cli (>=1.11)", "sphinx-autodoc-typehints (>=1.20.1)", "sphinx-copybutton (>=0.5.1)", "sphinx-inline-tabs (>=2022.1.2b11)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"] +testing = ["build[virtualenv] (>=0.9)", "covdefaults (>=2.2.2)", "devpi-process (>=0.3)", "diff-cover (>=7.3)", "distlib (>=0.3.6)", "flaky (>=3.7)", "hatch-vcs (>=0.3)", "hatchling (>=1.12.2)", "psutil (>=5.9.4)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest-xdist (>=3.1)", "re-assert (>=1.1)", "time-machine (>=2.8.2)", "wheel (>=0.38.4)"] [[package]] name = "types-aiofiles" -version = "22.1.0.4" +version = "22.1.0.6" description = "Typing stubs for aiofiles" category = "dev" optional = false python-versions = "*" files = [ - {file = "types-aiofiles-22.1.0.4.tar.gz", hash = "sha256:54465417fdfafc723e6f0fca66de5498866f1cf2595b72c9da35c96d1c3e9fce"}, - {file = "types_aiofiles-22.1.0.4-py3-none-any.whl", hash = "sha256:3c3d389ceec04c78bd33d13304332dcc46856a418d7d4ebf95e398f1efa3a3b7"}, + {file = "types-aiofiles-22.1.0.6.tar.gz", hash = "sha256:4399a20ff93f81dd4cc9ac25a76e0c508cd5bbccc0b1b6f972129213c9560b97"}, + {file = "types_aiofiles-22.1.0.6-py3-none-any.whl", hash = "sha256:416d5299b28b5070126b6618a6714e70d7bacb6082cc83aa19432d868f67b0d8"}, ] [[package]] @@ -1545,14 +1555,14 @@ files = [ [[package]] name = "urllib3" -version = "1.26.13" +version = "1.26.14" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ - {file = "urllib3-1.26.13-py2.py3-none-any.whl", hash = "sha256:47cc05d99aaa09c9e72ed5809b60e7ba354e64b59c9c173ac3018642d8bb41fc"}, - {file = "urllib3-1.26.13.tar.gz", hash = "sha256:c083dd0dce68dbfbe1129d5271cb90f9447dea7d52097c6e0126120c521ddea8"}, + {file = "urllib3-1.26.14-py2.py3-none-any.whl", hash = "sha256:75edcdc2f7d85b137124a6c3c9fc3933cdeaa12ecb9a6a959f22797a0feca7e1"}, + {file = "urllib3-1.26.14.tar.gz", hash = "sha256:076907bf8fd355cde77728471316625a4d2f7e713c125f51953bb5b3eecf4f72"}, ] [package.extras] @@ -1562,27 +1572,27 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "virtualenv" -version = "20.17.1" +version = "20.19.0" description = "Virtual Python Environment builder" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" files = [ - {file = "virtualenv-20.17.1-py3-none-any.whl", hash = "sha256:ce3b1684d6e1a20a3e5ed36795a97dfc6af29bc3970ca8dab93e11ac6094b3c4"}, - {file = "virtualenv-20.17.1.tar.gz", hash = "sha256:f8b927684efc6f1cc206c9db297a570ab9ad0e51c16fa9e45487d36d1905c058"}, + {file = "virtualenv-20.19.0-py3-none-any.whl", hash = "sha256:54eb59e7352b573aa04d53f80fc9736ed0ad5143af445a1e539aada6eb947dd1"}, + {file = "virtualenv-20.19.0.tar.gz", hash = "sha256:37a640ba82ed40b226599c522d411e4be5edb339a0c0de030c0dc7b646d61590"}, ] [package.dependencies] distlib = ">=0.3.6,<1" filelock = ">=3.4.1,<4" -platformdirs = ">=2.4,<3" +platformdirs = ">=2.4,<4" [package.extras] -docs = ["proselint (>=0.13)", "sphinx (>=5.3)", "sphinx-argparse (>=0.3.2)", "sphinx-rtd-theme (>=1)", "towncrier (>=22.8)"] -testing = ["coverage (>=6.2)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=21.3)", "pytest (>=7.0.1)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.6.1)", "pytest-randomly (>=3.10.3)", "pytest-timeout (>=2.1)"] +docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"] +test = ["covdefaults (>=2.2.2)", "coverage (>=7.1)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23)", "pytest (>=7.2.1)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)"] [[package]] -name = "Werkzeug" +name = "werkzeug" version = "2.2.2" description = "The comprehensive WSGI web application library." category = "main" @@ -1704,21 +1714,21 @@ multidict = ">=4.0" [[package]] name = "zipp" -version = "3.11.0" +version = "3.12.1" description = "Backport of pathlib-compatible object wrapper for zip files" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "zipp-3.11.0-py3-none-any.whl", hash = "sha256:83a28fcb75844b5c0cdaf5aa4003c2d728c77e05f5aeabe8e95e56727005fbaa"}, - {file = "zipp-3.11.0.tar.gz", hash = "sha256:a7a22e05929290a67401440b39690ae6563279bced5f314609d9d03798f56766"}, + {file = "zipp-3.12.1-py3-none-any.whl", hash = "sha256:6c4fe274b8f85ec73c37a8e4e3fa00df9fb9335da96fb789e3b96b318e5097b3"}, + {file = "zipp-3.12.1.tar.gz", hash = "sha256:a3cac813d40993596b39ea9e93a18e8a2076d5c378b8bc88ec32ab264e04ad02"}, ] [package.extras] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"] +docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] [metadata] lock-version = "2.0" python-versions = "^3.8.1" -content-hash = "47d783eb59ea6f88304d5c439b4bebf2c095b9d6a47f080d7c2def16cbda0095" +content-hash = "41e32881c249b1a1c9251e7b0b0937212eca7b7677e83ad3376eb7bd8fe22a34" diff --git a/pyproject.toml b/pyproject.toml index dae5a9c..8b0d1f2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,7 +23,7 @@ aiodns = "^3.0.0" aiofiles = "^22.1.0" aiohttp = "^3.8.3" quart = "^0.18.3" -bento-lib = {extras = ["quart"], version = "^5.2.0"} +bento-lib = {extras = ["quart"], version = "^5.4.0"} [tool.poetry.group.dev.dependencies] codecov = "^2.1.12" From ae7be66891224b922030a18b213078963913b7e2 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 7 Feb 2023 17:09:39 -0500 Subject: [PATCH 18/20] ci: bump bba to 0.10.1 --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 1d30ecf..73c382b 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -22,7 +22,7 @@ jobs: uses: actions/checkout@v3 - name: Run Bento build action - uses: bento-platform/bento_build_action@v0.6 + uses: bento-platform/bento_build_action@v0.10.1 with: registry: ghcr.io registry-username: ${{ github.actor }} From 66b09494a79bb44c1b6b2636a2bf15274a9b1b16 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 7 Feb 2023 17:09:58 -0500 Subject: [PATCH 19/20] chore: refact git info for service-info and include commit --- bento_service_registry/routes.py | 37 ++++++++++++++------------------ 1 file changed, 16 insertions(+), 21 deletions(-) diff --git a/bento_service_registry/routes.py b/bento_service_registry/routes.py index b3ffa5f..fbfd87a 100644 --- a/bento_service_registry/routes.py +++ b/bento_service_registry/routes.py @@ -166,6 +166,13 @@ async def service_types() -> quart.Response: return json.jsonify(list(types_by_key.values())) +async def _git_stdout(*args) -> str: + git_proc = await asyncio.create_subprocess_exec( + "git", *args, stdout=asyncio.subprocess.PIPE, stderr=asyncio.subprocess.PIPE) + res, _ = await git_proc.communicate() + return res.decode().rstrip() + + async def get_service_info() -> GA4GHServiceInfo: service_id = current_app.config["SERVICE_ID"] service_info_dict: GA4GHServiceInfo = { @@ -192,27 +199,15 @@ async def get_service_info() -> GA4GHServiceInfo: service_info_dict["environment"] = "dev" try: - git_proc = await asyncio.create_subprocess_exec( - "git", "describe", "--tags", "--abbrev=0", - stdout=asyncio.subprocess.PIPE, - stderr=asyncio.subprocess.PIPE, - ) - res_tag, _ = await git_proc.communicate() - if res_tag: - res_tag_str: str = res_tag.decode().rstrip() - service_info_dict["git_tag"] = res_tag_str - service_info_dict["bento"]["gitTag"] = res_tag_str - - git_proc = await asyncio.create_subprocess_exec( - "git", "branch", "--show-current", - stdout=asyncio.subprocess.PIPE, - stderr=asyncio.subprocess.PIPE, - ) - res_branch, _ = await git_proc.communicate() - if res_branch: - res_branch_str: str = res_branch.decode().rstrip() - service_info_dict["git_branch"] = res_branch_str - service_info_dict["bento"]["gitBranch"] = res_branch_str + if res_tag := await _git_stdout("describe", "--tags", "--abbrev=0"): + # noinspection PyTypeChecker + service_info_dict["bento"]["gitTag"] = res_tag + if res_branch := await _git_stdout("branch", "--show-current"): + # noinspection PyTypeChecker + service_info_dict["bento"]["gitBranch"] = res_branch + if res_commit := await _git_stdout("rev-parse", "HEAD"): + # noinspection PyTypeChecker + service_info_dict["bento"]["gitCommit"] = res_commit except Exception as e: except_name = type(e).__name__ From cd620cd74a089219543d088e5f1ff9d71e42acd3 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 8 Feb 2023 10:32:28 -0500 Subject: [PATCH 20/20] chore: chord -> bento --- bento_service_registry/app.py | 2 +- tests/{chord_services.json => bento_services.json} | 0 tests/conftest.py | 4 ++-- 3 files changed, 3 insertions(+), 3 deletions(-) rename tests/{chord_services.json => bento_services.json} (100%) diff --git a/bento_service_registry/app.py b/bento_service_registry/app.py index df44647..0a034f5 100644 --- a/bento_service_registry/app.py +++ b/bento_service_registry/app.py @@ -36,7 +36,7 @@ def create_app(): app.config.from_mapping( BENTO_DEBUG=bento_debug, BENTO_VALIDATE_SSL=validate_ssl, - BENTO_SERVICES=os.environ.get("CHORD_SERVICES", os.environ.get("BENTO_SERVICES", "chord_services.json")), + BENTO_SERVICES=os.environ.get("CHORD_SERVICES", os.environ.get("BENTO_SERVICES", "bento_services.json")), BENTO_URL=bento_url, BENTO_PUBLIC_URL=os.environ.get("BENTO_PUBLIC_URL", bento_url), BENTO_PORTAL_PUBLIC_URL=os.environ.get("BENTO_PORTAL_PUBLIC_URL", bento_url), diff --git a/tests/chord_services.json b/tests/bento_services.json similarity index 100% rename from tests/chord_services.json rename to tests/bento_services.json diff --git a/tests/conftest.py b/tests/conftest.py index 130125d..ed6e39a 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -5,9 +5,9 @@ def _setup_env(debug_mode: bool = False): - os.environ["CHORD_SERVICES"] = os.path.join(os.path.dirname(__file__), "chord_services.json") + os.environ["BENTO_SERVICES"] = os.path.join(os.path.dirname(__file__), "bento_services.json") os.environ["URL_PATH_FORMAT"] = "" # Mount off of root URL for testing - os.environ["CHORD_DEBUG"] = "true" if debug_mode else "" + os.environ["BENTO_DEBUG"] = "true" if debug_mode else "" @pytest.fixture()