diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 79955f01a..4a9dfb1af 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -28,3 +28,10 @@ jobs: test-folder: 'tests/integration' base-folder: 'astroobject' codecov-flags: "" + magstats_tests: + uses: ./.github/workflows/test_template.yaml + with: + python-version: '3.11' + sources-folder: 'magstats' + test-folder: 'tests' + base-folder: 'magstats' diff --git a/magstats/Dockerfile b/magstats/Dockerfile new file mode 100644 index 000000000..29499ee90 --- /dev/null +++ b/magstats/Dockerfile @@ -0,0 +1,30 @@ +FROM python:3.11 as python-base +LABEL org.opencontainers.image.authors="ALeRCE" +ENV PYTHONDONTWRITEBYTECODE=1 \ + PYTHONUNBUFFERED=1 \ + PYTHONFAULTHANDLER=1 \ + PIP_NO_CACHE_DIR=off \ + PIP_DISABLE_PIP_VERSION_CHECK=on \ + PIP_DEFAULT_TIMEOUT=100 \ + POETRY_VIRTUALENVS_IN_PROJECT=true \ + POETRY_NO_INTERACTION=1 + + +FROM python-base as builder +RUN pip install poetry +WORKDIR /app +COPY ./poetry.lock ./pyproject.toml /app +RUN poetry install --no-root --without=dev + + +FROM python:3.11-slim as production +RUN pip install poetry +COPY --from=builder /app /app +WORKDIR /app +COPY ./README.md /app/README.md +COPY ./entrypoint.sh /app/ +COPY ./core /app/core +COPY ./api /app/api +COPY ./database /app/database +RUN poetry install --only-root +CMD ["bash", "entrypoint.sh"] \ No newline at end of file diff --git a/magstats/README.md b/magstats/README.md new file mode 100644 index 000000000..e69de29bb diff --git a/magstats/api/__init__.py b/magstats/api/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/magstats/api/api.py b/magstats/api/api.py new file mode 100644 index 000000000..31c211a8e --- /dev/null +++ b/magstats/api/api.py @@ -0,0 +1,23 @@ +import os +from fastapi.middleware.cors import CORSMiddleware +from fastapi import FastAPI +from .routes import router +from prometheus_fastapi_instrumentator import Instrumentator + +app = FastAPI() +instrumentator = Instrumentator().instrument(app) + +app.add_middleware( + CORSMiddleware, + allow_origins=["*"], + allow_credentials=True, + allow_methods=["*"], + allow_headers=["*"], +) + +app.include_router(router) + + +@app.on_event("startup") +async def _startup(): + instrumentator.expose(app) diff --git a/magstats/api/result_handler.py b/magstats/api/result_handler.py new file mode 100644 index 000000000..d266fb1dd --- /dev/null +++ b/magstats/api/result_handler.py @@ -0,0 +1,27 @@ +from fastapi import HTTPException +from core.exceptions import ( + DatabaseError, + OidError, +) +import logging + + +def handle_success(result): + return result + + +def handle_error(err: Exception): + if isinstance(err, DatabaseError): + _handle_server_error(err) + if isinstance(err, OidError): + _handle_client_error(err) + + +def _handle_server_error(err: Exception): + logging.error(err) + raise HTTPException(status_code=500, detail=str(err)) + + +def _handle_client_error(err: Exception): + print(str(err)) + raise HTTPException(status_code=400, detail=str(err)) diff --git a/magstats/api/routes.py b/magstats/api/routes.py new file mode 100644 index 000000000..bd2196e5f --- /dev/null +++ b/magstats/api/routes.py @@ -0,0 +1,24 @@ +from fastapi import Request, APIRouter +from core.service import get_magstats +from .result_handler import handle_success, handle_error +from database.sql import session + +router = APIRouter() + + +@router.get("/") +def root(): + return "this is the magstats module" + + +@router.get("/magstats/{oid}") +def magstats( + request: Request, + oid: str, +): + return get_magstats( + oid=oid, + session_factory=session, + handle_success=handle_success, + handle_error=handle_error, + ) diff --git a/magstats/core/exceptions.py b/magstats/core/exceptions.py new file mode 100644 index 000000000..fbab11e41 --- /dev/null +++ b/magstats/core/exceptions.py @@ -0,0 +1,22 @@ +class WrapperException(BaseException): + def __init__(self, original_e, subcode=None): + super().__init__() + self.original_exception = original_e + self.subcode = subcode + + def __str__(self) -> str: + return self.original_exception.__str__() + + +class DatabaseError(WrapperException): + def __init__(self, original_e, subcode=None): + super().__init__(original_e, subcode) + + +class OidError(BaseException): + def __init__(self, oid) -> None: + super().__init__() + self.oid = oid + + def __str__(self) -> str: + return f"Can't retrieve magstats oid not recognized {self.oid}" diff --git a/magstats/core/models.py b/magstats/core/models.py new file mode 100644 index 000000000..cdb4c18f6 --- /dev/null +++ b/magstats/core/models.py @@ -0,0 +1,33 @@ +from pydantic import BaseModel, Field + + +class MagstatsModel(BaseModel): + fid: int = Field(description="Filter ID (1=g; 2=r, 3=i)") + stellar: bool = Field( + description="Whether the object appears to be unresolved in the given band" + ) + corrected: bool = Field( + description="Whether the corrected photometry should be used" + ) + ndet: int = Field(description="Number of detections in the given band") + ndubious: int = Field(description="Number of dubious corrections") + magmean: float = Field(description="The mean magnitude for the given fid") + magmedian: float = Field( + description="The median magnitude for the given fid" + ) + magmax: float = Field(description="The max magnitude for the given fid") + magmin: float = Field(description="The min magnitude for the given fid") + magsigma: float = Field( + description="Magnitude standard deviation for the given fid" + ) + maglast: float = Field(description="The last magnitude for the given fid") + magfirst: float = Field( + description="The first magnitude for the given fid" + ) + firstmjd: float = Field( + description="The time of the first detection in the given fid" + ) + lastmjd: float = Field( + description="The time of the last detection in the given fid" + ) + step_id_corr: str = Field(description="Correction step pipeline version") diff --git a/magstats/core/service.py b/magstats/core/service.py new file mode 100644 index 000000000..8b0f2cb44 --- /dev/null +++ b/magstats/core/service.py @@ -0,0 +1,51 @@ +from contextlib import AbstractContextManager +from typing import Callable +from .models import MagstatsModel +from pymongo.database import Database +from sqlalchemy.orm import Session +from .exceptions import DatabaseError, OidError +from db_plugins.db.sql import models +from sqlalchemy import select, text + + +def default_handle_success(result): + return result + + +def default_handle_error(error): + raise error + + +def get_magstats( + oid: str, + session_factory: Callable[..., AbstractContextManager[Session]] = None, + handle_success: Callable[..., dict] = default_handle_success, + handle_error: Callable[Exception, None] = default_handle_error, +): + result = _get_magstats_sql(session_factory, oid, handle_error) + if len(result) == 0: + handle_error(OidError(oid)) + else: + print(result) + return handle_success(result) + + +def _get_magstats_sql( + session_factory: Callable[..., AbstractContextManager[Session]], + oid: str, + handle_error: Callable[Exception, None] = default_handle_error, +): + try: + with session_factory() as session: + stmt = select(models.MagStats, text("'ztf'")).filter( + models.MagStats.oid == oid + ) + result = session.execute(stmt) + result = [ + MagstatsModel(**ob[0].__dict__, tid=ob[1]) + for ob in result.all() + ] + return result + + except Exception as e: + return handle_error(DatabaseError(e)) diff --git a/magstats/database/__init__.py b/magstats/database/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/magstats/database/sql.py b/magstats/database/sql.py new file mode 100644 index 000000000..e9f81f7b1 --- /dev/null +++ b/magstats/database/sql.py @@ -0,0 +1,36 @@ +from contextlib import contextmanager, AbstractContextManager +import logging +import os +from typing import Callable +from sqlalchemy.orm import scoped_session, sessionmaker, Session +from sqlalchemy.engine import Engine, create_engine + + +logger = logging.getLogger(__name__) + + +user = os.getenv("PSQL_USER") +pwd = os.getenv("PSQL_PASSWORD") +host = os.getenv("PSQL_HOST") +port = os.getenv("PSQL_PORT") +db = os.getenv("PSQL_DATABASE") +db_url = f"postgresql://{user}:{pwd}@{host}:{port}/{db}" + +engine: Engine = create_engine(db_url, echo=False) + + +@contextmanager +def session() -> Callable[..., AbstractContextManager[Session]]: + session_factory = scoped_session( + sessionmaker(autocommit=False, autoflush=False, bind=engine) + ) + session: Session = session_factory() + try: + yield session + except Exception: + logger.debug("Connecting databases") + logger.exception("Session rollback because of exception") + session.rollback() + raise + finally: + session.close() diff --git a/magstats/dist/magstats-0.1.0-py3-none-any.whl b/magstats/dist/magstats-0.1.0-py3-none-any.whl new file mode 100644 index 000000000..96578a826 Binary files /dev/null and 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b/magstats/pyproject.toml new file mode 100644 index 000000000..fc85ef5be --- /dev/null +++ b/magstats/pyproject.toml @@ -0,0 +1,37 @@ +[tool.poetry] +name = "magstats" +version = "0.1.0" +description = "Get Magstats of objects from ZTF and ATLAS surveys" +authors = ["mmolina2018 "] +readme = "README.md" +packages = [{include = "core"}, {include = "api"}, {include = "database"}] + +[tool.poetry.dependencies] +fastapi = "^0.100.0" +python = "^3.11" +sqlalchemy = {extras = ["asyncio"], version = "^2.0.19"} +returns = "^0.21.0" +psycopg2-binary = "^2.9.6" +db-plugins = { version = "5.1.1", python = ">=3.11,<3.12"} +prometheus-fastapi-instrumentator = "^6.1.0" + +[tool.poetry.group.dev.dependencies] +pytest = "^7.4.0" +pytest-docker = "^2.0.0" +black = "^23.7.0" +pytest-cov = "^4.1.0" +pytest-asyncio = "^0.21.1" +httpx = "^0.24.1" + +[tool.poetry.group.production.dependencies] +uvicorn = {extras = ["standard"], version = "^0.23.1"} + +[tool.poetry.group.profiling.dependencies] +memray = "^1.8.1" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" + +[tool.black] +line-length = 79 diff --git a/magstats/tests/conftest.py b/magstats/tests/conftest.py new file mode 100644 index 000000000..6965d1046 --- /dev/null +++ b/magstats/tests/conftest.py @@ -0,0 +1,169 @@ +import pytest +import os +import pathlib +import psycopg2 +from db_plugins.db.sql._connection import PsqlDatabase as DbpDatabase +from fastapi.testclient import TestClient +from db_plugins.db.sql.models import Object, MagStats + + +@pytest.fixture(scope="session") +def docker_compose_command(): + compose_version = os.getenv("COMPOSE_VERSION", "v1") + if compose_version == "v1": + return "docker-compose" + return "docker compose" + + +@pytest.fixture(scope="session") +def docker_compose_file(pytestconfig): + try: + path = pathlib.Path(pytestconfig.rootdir) / "tests/docker-compose.yml" + assert path.exists() + return path + except AssertionError: + path = ( + pathlib.Path(pytestconfig.rootdir) + / "magstats/tests/docker-compose.yml" + ) + assert path.exists() + return path + + +def is_responsive_psql(url): + try: + conn = psycopg2.connect( + "dbname='postgres' user='postgres' host=localhost password='postgres'" + ) + conn.close() + return True + except Exception: + return False + + +@pytest.fixture(scope="session") +def psql_service(docker_ip, docker_services): + """Ensure that Kafka service is up and responsive.""" + # `port_for` takes a container port and returns the corresponding host port + port = docker_services.port_for("postgres", 5432) + server = "{}:{}".format(docker_ip, port) + docker_services.wait_until_responsive( + timeout=30.0, pause=0.1, check=lambda: is_responsive_psql(server) + ) + return server + + +@pytest.fixture +def init_psql(): + user = "postgres" + pwd = "postgres" + host = "localhost" + port = "5432" + db = "postgres" + config = { + "USER": user, + "PASSWORD": pwd, + "HOST": host, + "PORT": port, + "DB_NAME": db, + } + dbp_database = DbpDatabase(config) + populate_psql(dbp_database) + yield dbp_database + teardown_psql(dbp_database) + + +@pytest.fixture +def psql_session(): + os.environ["PSQL_PORT"] = "5432" + os.environ["PSQL_HOST"] = "localhost" + os.environ["PSQL_USER"] = "postgres" + os.environ["PSQL_PASSWORD"] = "postgres" + os.environ["PSQL_DATABASE"] = "postgres" + from database.sql import session + + return session + + +def populate_psql(database): + database.create_db() + with database.session() as session: + add_psql_objects(session) + add_psql_magstats(session) + + +def add_psql_objects(session): + object = Object(oid="oid1") + object2 = Object(oid="oid2") + session.add(object) + session.add(object2) + session.commit() + + +def add_psql_magstats(session): + magstats = [ + { + "fid": 123, + "oid": "oid1", + "stellar": False, + "corrected": False, + "ndet": 1, + "ndubious": 1, + "dmdt_first": 0.13, + "dm_first": 0.12, + "sigmadm_first": 1.4, + "dt_first": 2.0, + "magmean": 19.0, + "magmedian": 20, + "magmax": 1.4, + "magmin": 1.4, + "magsigma": 1.4, + "maglast": 1.4, + "magfirst": 1.4, + "firstmjd": 1.4, + "lastmjd": 1.4, + "step_id_corr": "test", + }, + { + "fid": 456, + "oid": "oid2", + "stellar": False, + "corrected": False, + "ndet": 1, + "ndubious": 1, + "dmdt_first": 0.13, + "dm_first": 0.12, + "sigmadm_first": 1.4, + "dt_first": 2.0, + "magmean": 19.0, + "magmedian": 20, + "magmax": 1.4, + "magmin": 1.4, + "magsigma": 1.4, + "maglast": 1.4, + "magfirst": 1.4, + "firstmjd": 1.4, + "lastmjd": 1.4, + "step_id_corr": "test", + }, + ] + magstats = [MagStats(**mag) for mag in magstats] + session.add_all(magstats) + session.commit() + + +def teardown_psql(database): + database.drop_db() + + +@pytest.fixture(scope="session") +def test_client(): + os.environ["PSQL_PORT"] = "5432" + os.environ["PSQL_HOST"] = "localhost" + os.environ["PSQL_USER"] = "postgres" + os.environ["PSQL_PASSWORD"] = "postgres" + os.environ["PSQL_DATABASE"] = "postgres" + os.environ["SECRET_KEY"] = "some_secret" + from api.api import app + + return TestClient(app) diff --git a/magstats/tests/docker-compose.yml b/magstats/tests/docker-compose.yml new file mode 100644 index 000000000..519eeec85 --- /dev/null +++ b/magstats/tests/docker-compose.yml @@ -0,0 +1,10 @@ +version: "3" +services: + postgres: + image: postgres + environment: + - POSTGRES_USER=postgres + - POSTGRES_DB=postgres + - POSTGRES_PASSWORD=postgres + ports: + - 5432:5432 diff --git a/magstats/tests/profiling/docker-compose.yaml b/magstats/tests/profiling/docker-compose.yaml new file mode 100644 index 000000000..8b12dab01 --- /dev/null +++ b/magstats/tests/profiling/docker-compose.yaml @@ -0,0 +1,31 @@ +version: "3" +services: + #postgres database for alerts + postgres: + image: postgres + environment: + - POSTGRES_USER=postgres + - POSTGRES_DB=postgres + - POSTGRES_PASSWORD=postgres + ports: + - 5432:5432 + + magstats_api: + build: + context: ../../../ + dockerfile: ./magstats/Dockerfile + ports: + - 5001:5001 + command: bash tests/profiling/entrypoint.sh + environment: + - PORT=5001 + - PSQL_HOST=postgres + - PSQL_DATABASE=postgres + - PSQL_USER=postgres + - PSQL_PASSWORD=postgres + - PSQL_PORT=5432 + - CONNECT_PSQL=YES + - LOG_LEVEL=DEBUG + - SECRET_KEY=a_secret_key + volumes: + - ./:/app/tests/profiling \ No newline at end of file diff --git a/magstats/tests/profiling/entrypoint.sh b/magstats/tests/profiling/entrypoint.sh new file mode 100644 index 000000000..8eb489013 --- /dev/null +++ b/magstats/tests/profiling/entrypoint.sh @@ -0,0 +1 @@ +poetry run memray run -o /app/tests/profiling/memray_graph.bin --follow-fork -m uvicorn --host 0.0.0.0 --port $PORT api.api:app \ No newline at end of file diff --git a/magstats/tests/profiling/initdb.py b/magstats/tests/profiling/initdb.py new file mode 100644 index 000000000..f155b5c25 --- /dev/null +++ b/magstats/tests/profiling/initdb.py @@ -0,0 +1,90 @@ +from db_plugins.db.sql._connection import PsqlDatabase +from db_plugins.db.sql.models import Object, MagStats + + +def database(): + user = "postgres" + pwd = "postgres" + host = "localhost" + port = "5432" + db = "postgres" + database = PsqlDatabase( + { + "USER": user, + "PASSWORD": pwd, + "HOST": host, + "PORT": int(port), + "DB_NAME": db, + } + ) + return database + + +def populate_databases(database): + database.create_db() + with database.session() as session: + object1 = Object(oid="oid1") + object2 = Object(oid="oid2") + session.add_all([object1, object2]) + session.commit() + magstats1 = [ + { + "fid": 123, + "oid": "oid1", + "stellar": False, + "corrected": False, + "ndet": 1, + "ndubious": 1, + "dmdt_first": 0.13, + "dm_first": 0.12, + "sigmadm_first": 1.4, + "dt_first": 2.0, + "magmean": 19.0, + "magmedian": 20, + "magmax": 1.4, + "magmin": 1.4, + "magsigma": 1.4, + "maglast": 1.4, + "magfirst": 1.4, + "firstmjd": 1.4, + "lastmjd": 1.4, + "step_id_corr": "test", + } + ] + magstats2 = [ + { + "fid": 456, + "oid": "oid2", + "stellar": False, + "corrected": False, + "ndet": 1, + "ndubious": 1, + "dmdt_first": 0.13, + "dm_first": 0.12, + "sigmadm_first": 1.4, + "dt_first": 2.0, + "magmean": 19.0, + "magmedian": 20, + "magmax": 1.4, + "magmin": 1.4, + "magsigma": 1.4, + "maglast": 1.4, + "magfirst": 1.4, + "firstmjd": 1.4, + "lastmjd": 1.4, + "step_id_corr": "test", + } + ] + + session.add_all(magstats1) + session.add_all(magstats2) + session.commit() + + +def teardown_databases(database: PsqlDatabase): + database.drop_db() + + +if __name__ == "__main__": + db = database() + populate_databases(db) diff --git a/magstats/tests/profiling/loadtest.py b/magstats/tests/profiling/loadtest.py new file mode 100644 index 000000000..71e7e4736 --- /dev/null +++ b/magstats/tests/profiling/loadtest.py @@ -0,0 +1,9 @@ +import subprocess + +for i in range(2): + oid = ["oid1", "oid2"] + subprocess.run( + f"hey -n 100 -c 8 http://localhost:5432/magstats/{oid[i%2]}".split( + " " + ), + ) diff --git a/magstats/tests/test_api.py b/magstats/tests/test_api.py new file mode 100644 index 000000000..e4cdebea4 --- /dev/null +++ b/magstats/tests/test_api.py @@ -0,0 +1,9 @@ +def test_root(test_client): + res = test_client.get("/") + assert res.status_code == 200 + + +def test_magstats_from_ztf(psql_service, init_psql, test_client): + res = test_client.get("/magstats/oid1") + assert res.status_code == 200 + assert res.json()[0]["fid"] == 123 diff --git a/magstats/tests/test_service.py b/magstats/tests/test_service.py new file mode 100644 index 000000000..30c0299bb --- /dev/null +++ b/magstats/tests/test_service.py @@ -0,0 +1,41 @@ +from core.service import get_magstats +from api.result_handler import handle_error +from fastapi import HTTPException +import pytest + + +def test_get_ztf_magstats(psql_service, psql_session, init_psql): + result = get_magstats( + session_factory=psql_session, + oid="oid1", + ) + assert result[0].fid == 123 + + +def test_get_magstats_from_unknown_oid(psql_service, psql_session, init_psql): + with pytest.raises(HTTPException) as exc: + get_magstats( + session_factory=psql_session, + oid="unknown", + handle_error=handle_error, + ) + + assert exc.value.status_code == 400 + assert ( + exc.value.detail + == "Can't retrieve magstats oid not recognized unknown" + ) + + + +def mock_session_factory_with_exception(): + raise Exception("Test exception") + +def test_get_magstats_with_db_exception(): + with pytest.raises(HTTPException) as exc: + get_magstats( + session_factory=mock_session_factory_with_exception, + oid="oid1", + handle_error=handle_error, + ) + assert exc.value.status_code == 500