From 4b51bb4871ce2f567fef0b3790f892a2afb079aa Mon Sep 17 00:00:00 2001 From: Vincent Sarago Date: Sat, 31 Aug 2024 01:06:25 +0200 Subject: [PATCH] refactor to ease usage and packaging (#32) * refactor to ease usage and packaging * Update .gitignore * add open=True to avoid deprecation * add compression middleware * switch to orjson * Use poetry for dependency management given lambda deployment * Update CI for poetry dependency management * Add pre-commit to poetry test dependencies * Run pip through python --------- Co-authored-by: Zachary Deziel --- .github/workflows/ci.yml | 38 +- .gitignore | 2 +- docker-compose.yaml | 11 +- space2stats_api/cdk/aws_stack.py | 2 +- space2stats_api/local_db.env | 6 - space2stats_api/pytest.ini | 2 - space2stats_api/src/LICENSE | 541 ++++++ space2stats_api/src/README.md | 1 + space2stats_api/src/app/__init__.py | 0 space2stats_api/src/app/main.py | 23 - space2stats_api/src/app/routers/__init__.py | 0 space2stats_api/src/app/routers/api.py | 59 - space2stats_api/src/app/settings.py | 16 - space2stats_api/src/app/utils/__init__.py | 0 space2stats_api/src/app/utils/db_utils.py | 60 - space2stats_api/src/poetry.lock | 1526 +++++++++++++++++ space2stats_api/src/pyproject.toml | 37 + space2stats_api/src/requirements.txt | 13 - space2stats_api/src/space2stats/__init__.py | 5 + space2stats_api/src/space2stats/__main__.py | 23 + space2stats_api/src/space2stats/app.py | 60 + space2stats_api/src/space2stats/db.py | 40 + .../{app/utils => space2stats}/h3_utils.py | 2 + space2stats_api/src/space2stats/handler.py | 22 + space2stats_api/src/space2stats/main.py | 139 ++ space2stats_api/src/space2stats/settings.py | 34 + space2stats_api/{ => src/tests}/__init__.py | 0 space2stats_api/{ => src}/tests/test_api.py | 55 +- .../{ => src}/tests/test_h3_utils.py | 2 +- space2stats_api/tests/__init__.py | 0 space2stats_api/tests/test_db_utils.py | 68 - 31 files changed, 2499 insertions(+), 288 deletions(-) delete mode 100644 space2stats_api/local_db.env delete mode 100644 space2stats_api/pytest.ini create mode 100644 space2stats_api/src/LICENSE create mode 100644 space2stats_api/src/README.md delete mode 100644 space2stats_api/src/app/__init__.py delete mode 100644 space2stats_api/src/app/main.py delete mode 100644 space2stats_api/src/app/routers/__init__.py delete mode 100644 space2stats_api/src/app/routers/api.py delete mode 100644 space2stats_api/src/app/settings.py delete mode 100644 space2stats_api/src/app/utils/__init__.py delete mode 100644 space2stats_api/src/app/utils/db_utils.py create mode 100644 space2stats_api/src/poetry.lock create mode 100644 space2stats_api/src/pyproject.toml delete mode 100644 space2stats_api/src/requirements.txt create mode 100644 space2stats_api/src/space2stats/__init__.py create mode 100644 space2stats_api/src/space2stats/__main__.py create mode 100644 space2stats_api/src/space2stats/app.py create mode 100644 space2stats_api/src/space2stats/db.py rename space2stats_api/src/{app/utils => space2stats}/h3_utils.py (99%) create mode 100644 space2stats_api/src/space2stats/handler.py create mode 100644 space2stats_api/src/space2stats/main.py create mode 100644 space2stats_api/src/space2stats/settings.py rename space2stats_api/{ => src/tests}/__init__.py (100%) rename space2stats_api/{ => src}/tests/test_api.py (72%) rename space2stats_api/{ => src}/tests/test_h3_utils.py (96%) delete mode 100644 space2stats_api/tests/__init__.py delete mode 100644 space2stats_api/tests/test_db_utils.py diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c0f436b..0e2775f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -6,34 +6,38 @@ jobs: test: runs-on: ubuntu-latest - env: - DB_HOST: localhost - DB_PORT: 5432 - DB_NAME: mydatabase - DB_USER: myuser - DB_PASSWORD: mypassword - DB_TABLE_NAME: space2stats - steps: - name: Checkout code - uses: actions/checkout@v2 + uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: 3.11 - - name: Install dependencies + - name: Install Poetry run: | python -m pip install --upgrade pip - pip install -r space2stats_api/src/requirements.txt - pip install pre-commit pytest + python -m pip install poetry - - name: Set PYTHONPATH - run: echo "PYTHONPATH=$(pwd)/space2stats_api" >> $GITHUB_ENV + - name: Install dependencies + working-directory: ./space2stats_api/src + run: | + poetry install --with test - name: Run pre-commit - run: pre-commit run --all-files + working-directory: ./space2stats_api/src + run: | + poetry run pre-commit run --all-files - name: Run tests - run: pytest space2stats_api/tests \ No newline at end of file + working-directory: ./space2stats_api/src + run: | + poetry run pytest -s -vv + env: + DB_HOST: localhost + DB_PORT: 5432 + DB_NAME: mydatabase + DB_USER: myuser + DB_PASSWORD: mypassword + DB_TABLE_NAME: space2stats \ No newline at end of file diff --git a/.gitignore b/.gitignore index 4edf48e..22a2476 100644 --- a/.gitignore +++ b/.gitignore @@ -104,4 +104,4 @@ db.env space2stats_api/space2stats_env *.env cdk.out -lambda_layer \ No newline at end of file +lambda_layer diff --git a/docker-compose.yaml b/docker-compose.yaml index 4867b63..f4cfe02 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -2,16 +2,17 @@ version: '3' services: database: - image: ghcr.io/stac-utils/pgstac:v0.8.5 + # at time of writing this, ARM64 is not supported so we make sure to use + # a supported platform: https://github.com/postgis/docker-postgis/issues/216 + # Could possibly switch to https://github.com/vincentsarago/containers + platform: linux/amd64 + image: postgis/postgis:15-3.4 environment: - POSTGRES_USER=username - POSTGRES_PASSWORD=password - POSTGRES_DB=postgis - - PGUSER=username - - PGPASSWORD=password - - PGDATABASE=postgis ports: - "${MY_DOCKER_IP:-127.0.0.1}:5439:5432" command: postgres -N 500 volumes: - - ./.pgdata:/var/lib/postgresql/data \ No newline at end of file + - ./.pgdata:/var/lib/postgresql/data diff --git a/space2stats_api/cdk/aws_stack.py b/space2stats_api/cdk/aws_stack.py index eaec78f..208f967 100644 --- a/space2stats_api/cdk/aws_stack.py +++ b/space2stats_api/cdk/aws_stack.py @@ -19,7 +19,7 @@ def __init__(self, scope: Construct, id: str, **kwargs) -> None: self, "Space2StatsFunction", entry="../src", runtime=_lambda.Runtime.PYTHON_3_11, - index="app/main.py", + index="space2stats/handler.py", timeout=Duration.seconds(120), handler="handler", environment=app_settings.model_dump(), diff --git a/space2stats_api/local_db.env b/space2stats_api/local_db.env deleted file mode 100644 index b392777..0000000 --- a/space2stats_api/local_db.env +++ /dev/null @@ -1,6 +0,0 @@ -DB_HOST=localhost -DB_PORT=5439 -DB_NAME=postgis -DB_USER=username -DB_PASSWORD=password -DB_TABLE_NAME=space2stats \ No newline at end of file diff --git a/space2stats_api/pytest.ini b/space2stats_api/pytest.ini deleted file mode 100644 index 343729c..0000000 --- a/space2stats_api/pytest.ini +++ /dev/null @@ -1,2 +0,0 @@ -[pytest] -env_files = db.env \ No newline at end of file diff --git a/space2stats_api/src/LICENSE b/space2stats_api/src/LICENSE new file mode 100644 index 0000000..e605458 --- /dev/null +++ b/space2stats_api/src/LICENSE @@ -0,0 +1,541 @@ +World Bank Master Community License Agreement + +THIS WORLD BANK COMMUNITY LICENSE AGREEMENT ("Agreement") is entered +between the International Bank for Reconstruction and +Development/International Development Association ("World Bank") +and the party identified as licensee on the signature page of this +Agreement ("Licensee"). Licensee and the World Bank are each referred to +herein as a "Party" and collectively as, the "Parties". + +A. The World Bank has developed that certain computer software + identified on Exhibit B ("Licensed Software") for use for the + public good and desire to make the Licensed Software available to + Licensee on a royalty-free basis, subject to certain other terms and + conditions. + +B. Licensee wishes to secure certain rights to use, modify and + sublicense the Licensed Software. + +NOW, THEREFORE, in consideration of the mutual promises of the Parties +and other good and valuable consideration, receipt of which is hereby +acknowledged, the Parties agree as follows: + +1. Definitions + + 1. **"Contribution"** means any subject matter which is created by + any person, which subject matter has the effect of adding to, + deleting from, replacing, or otherwise modifying the text, + binary or other material in a Core Program, whether deriving + directly from a Core Program or from Licensed Software. 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Obligations of Licensee + + 1. **Distribution of Source Code.** In the event that Licensee + Distributes any form of the Licensed Software, whether as Source + Code or Object Code and whether by itself or as part of a + Covered Work, Licensee shall promptly make available the full + Source Code of such Licensed Software (including any + Contributions by Licensee) to all persons on the terms set forth + in Exhibit A, either by making such Source Code accessible in a + commonly available online source code repository, an online + repository under the direct control of Licensee, or by notifying + such persons that such Source Code may be delivered by + electronic transmission to any requesting person, at no charge + other than a reasonable fee covering the cost of distribution to + the recipient. + + 2. **Inclusion of Applicable License Provisions.** Licensee shall + assure that every copy of Licensed Software (including any such + copy included in a Covered Work) shall either include the full + text of the license required by Section 3.2 or a statement that + identifies a uniform resource locator which contains the + applicable license. + + 3. **No Further Restrictions.** Licensee shall not impose any + restrictions on the further use, distribution or modification of + Licensed Software, whether distributed by itself or as part of a + Covered Work, provided that the License Software is made + available by Licensee and its sublicensee on terms specified in + Exhibit A hereto. 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A preamble as follows: + +By acquiring a copy of the Survey Solutions (the "Subject +Software"), the person so acquiring such copy, for himself/herself and +on behalf of his or her employer or principal (collectively, +"Licensee"), acknowledges and agrees that the exploitation of the +Subject Software is subject strictly to the terms and conditions of this +License Agreement, that Licensee is furthermore bound to perform all +obligations of Licensee in all material respects, and that this +Agreement may be enforced against Licensee by Licensor and/or any other +person or entity who holds the copyright to the Core Software, the +Licensed Software, or any Contribution thereto, as defined below. + +2. All definitions included in Article 1 of the Agreement. + +3. The following sections: + +**Basic Grant.** Subject to Licensee's compliance with all terms and +conditions of this Agreement, Licensor grants to Licensee the +royalty-free, perpetual, non-exclusive right and license to Exploit the +Licensed Software, whether alone or as part of a Covered Work. + +**Territorial Limitations.** The rights granted to Licensee hereunder +only apply to exploitation in the member countries of the World Bank +("Licensed Territory"). + +**Rights in Contributions.** Licensee hereby grants to Licensor and its +licensors a paid up, royalty-free, perpetual, irrevocable, +non-exclusive, sublicenseable right and license to Exploit any +Contributions created by or for Licensee, effective immediately on the +first Distribution of any work containing a Contribution. + +**Patent Rights.** Licensee further grants to Licensor and its licensors +and their respective licensees a paid up, royalty-free, perpetual, +irrevocable and sublicenseable license to Exploit its Contributions or +any version of the Licensed Software including its Contributions under +any patents now or in the future owned or licenseable by Licensee, +solely to the extent that such Exploitation is of a work consisting of +Licensed Software and Licensee's Contribution. + +**No Personal Use.** Licensee represents and warrants that the Licensed +Software is not intended to be used and will not be used or authorized +for use for personal, household and/or family uses. + +**Distribution of Source Code.** In the event that Licensee Distributes +any form of the Licensed Software, whether as Source Code or Object Code +and whether by itself or as part of a Covered Work, Licensee shall +promptly make available the full Source Code of such Licensed Software +(including any Contributions by Licensee) to all persons on the terms +set forth in this License Agreement, either by making such Source Code +accessible in a commonly available online source code repository, an +online repository under the direct control of Licensee, or by notifying +such persons that such Source Code may be delivered by electronic +transmission to any requesting person, at no charge other than a +reasonable fee covering the cost of distribution to the recipient. + +**Inclusion of Applicable License Provisions.** Licensee shall assure +that every copy of Licensed Software (including any such copy included +in a Covered Work) shall either include the full text of this license or +a statement that identifies a uniform resource locator which contains +the applicable license. + +**No Further Restrictions.** Licensee shall not impose any restrictions +on the further use, distribution or modification of Licensed Software, +whether distributed by itself or as part of a Covered Work, other than +the terms of this License. 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Notwithstanding the foregoing, The World Bank shall have +the right to seek interim, provisional or other equitable relief, +including temporary or permanent injunctive relief, as necessary to +protect its interests. diff --git a/space2stats_api/src/README.md b/space2stats_api/src/README.md new file mode 100644 index 0000000..d6a0904 --- /dev/null +++ b/space2stats_api/src/README.md @@ -0,0 +1 @@ +## space2stats diff --git a/space2stats_api/src/app/__init__.py b/space2stats_api/src/app/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/space2stats_api/src/app/main.py b/space2stats_api/src/app/main.py deleted file mode 100644 index 70e659d..0000000 --- a/space2stats_api/src/app/main.py +++ /dev/null @@ -1,23 +0,0 @@ -from fastapi import FastAPI -from fastapi.middleware.cors import CORSMiddleware -from mangum import Mangum - -from .routers import api - -app = FastAPI() - -app.add_middleware( - CORSMiddleware, - allow_origins=["*"], - allow_credentials=True, - allow_methods=["*"], - allow_headers=["*"], -) - -app.include_router(api.router) - -@app.get("/") -def read_root(): - return {"message": "Welcome to Space2Stats!"} - -handler = Mangum(app) diff --git a/space2stats_api/src/app/routers/__init__.py b/space2stats_api/src/app/routers/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/space2stats_api/src/app/routers/api.py b/space2stats_api/src/app/routers/api.py deleted file mode 100644 index ba9069e..0000000 --- a/space2stats_api/src/app/routers/api.py +++ /dev/null @@ -1,59 +0,0 @@ -from typing import Any, Dict, List, Literal, Optional, TypeAlias - -from fastapi import APIRouter -from geojson_pydantic import Feature, Polygon -from pydantic import BaseModel - -from ..utils.db_utils import get_available_fields, get_summaries -from ..utils.h3_utils import generate_h3_geometries, generate_h3_ids - -router = APIRouter() - -AOIModel: TypeAlias = Feature[Polygon, Dict] - - -class SummaryRequest(BaseModel): - aoi: AOIModel - spatial_join_method: Literal["touches", "centroid", "within"] - fields: List[str] - geometry: Optional[Literal["polygon", "point"]] = None - - -@router.post("/summary", response_model=List[Dict[str, Any]]) -def get_summary(request: SummaryRequest): - resolution = 6 - h3_ids = generate_h3_ids( - dict(request.aoi.geometry), resolution, request.spatial_join_method - ) - - if not h3_ids: - return [] - - rows, colnames = get_summaries(request.fields, h3_ids) - if not rows: - return [] - - summaries = [] - geometries = ( - generate_h3_geometries(h3_ids, request.geometry) if request.geometry else None - ) - - for idx, row in enumerate(rows): - summary = {"hex_id": row[0]} - if request.geometry and geometries: - summary["geometry"] = geometries[idx] - summary.update( - { - col: row[idx] - for idx, col in enumerate(colnames[1:], start=1) - if col in request.fields - } - ) - summaries.append(summary) - - return summaries - - -@router.get("/fields", response_model=List[str]) -def fields(): - return get_available_fields() diff --git a/space2stats_api/src/app/settings.py b/space2stats_api/src/app/settings.py deleted file mode 100644 index 9c07e99..0000000 --- a/space2stats_api/src/app/settings.py +++ /dev/null @@ -1,16 +0,0 @@ -from pydantic_settings import BaseSettings - - -class Settings(BaseSettings): - DB_HOST: str - DB_PORT: int - DB_NAME: str - DB_USER: str - DB_PASSWORD: str - DB_TABLE_NAME: str - - @property - def DB_CONNECTION_STRING(self) -> str: - host_port = f"host={self.DB_HOST} port={self.DB_PORT}" - db_user = f"dbname={self.DB_NAME} user={self.DB_USER}" - return f"{host_port} {db_user} password={self.DB_PASSWORD}" diff --git a/space2stats_api/src/app/utils/__init__.py b/space2stats_api/src/app/utils/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/space2stats_api/src/app/utils/db_utils.py b/space2stats_api/src/app/utils/db_utils.py deleted file mode 100644 index cc091b2..0000000 --- a/space2stats_api/src/app/utils/db_utils.py +++ /dev/null @@ -1,60 +0,0 @@ -import psycopg as pg -from psycopg_pool import ConnectionPool - -from ..settings import Settings - -settings = Settings() - -conninfo = settings.DB_CONNECTION_STRING -pool = ConnectionPool(conninfo=conninfo, min_size=1, max_size=10, open=True) - - -def get_summaries(fields, h3_ids): - colnames = ["hex_id"] + fields - cols = [pg.sql.Identifier(c) for c in colnames] - sql_query = pg.sql.SQL( - """ - SELECT {0} - FROM {1} - WHERE hex_id = ANY (%s) - """ - ).format(pg.sql.SQL(", ").join(cols), pg.sql.Identifier(settings.DB_TABLE_NAME)) - try: - # Convert h3_ids to a list to ensure compatibility with psycopg - h3_ids = list(h3_ids) - with pool.connection() as conn: - with conn.cursor() as cur: - cur.execute( - sql_query, - [ - h3_ids, - ], - ) - rows = cur.fetchall() - colnames = [desc[0] for desc in cur.description] - except Exception as e: - raise e - - return rows, colnames - - -def get_available_fields(): - sql_query = """ - SELECT column_name - FROM information_schema.columns - WHERE table_name = %s - """ - try: - with pool.connection() as conn: - with conn.cursor() as cur: - cur.execute( - sql_query, - [ - settings.DB_TABLE_NAME, - ], - ) - columns = [row[0] for row in cur.fetchall() if row[0] != "hex_id"] - except Exception as e: - raise e - - return columns diff --git a/space2stats_api/src/poetry.lock b/space2stats_api/src/poetry.lock new file mode 100644 index 0000000..3a5d1b9 --- /dev/null +++ b/space2stats_api/src/poetry.lock @@ -0,0 +1,1526 @@ +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. + +[[package]] +name = "annotated-types" +version = "0.7.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +files = [ + {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, + {file = "annotated_types-0.7.0.tar.gz", hash = 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+pre-commit = "*" +pytest = "*" +pytest-cov = "*" +pytest-postgresql = "*" + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" \ No newline at end of file diff --git a/space2stats_api/src/requirements.txt b/space2stats_api/src/requirements.txt deleted file mode 100644 index 1df06e9..0000000 --- a/space2stats_api/src/requirements.txt +++ /dev/null @@ -1,13 +0,0 @@ -fastapi -uvicorn -mangum -pandas -python-dotenv -shapely -h3 -psycopg[binary] -psycopg[pool] -httpx -geojson-pydantic -shapely -pydantic-settings>=2.0.0 diff --git a/space2stats_api/src/space2stats/__init__.py b/space2stats_api/src/space2stats/__init__.py new file mode 100644 index 0000000..2f11cf2 --- /dev/null +++ b/space2stats_api/src/space2stats/__init__.py @@ -0,0 +1,5 @@ +"""space2stats.""" + +from .main import fields, summaries # noqa + +__version__ = "0.1.0" diff --git a/space2stats_api/src/space2stats/__main__.py b/space2stats_api/src/space2stats/__main__.py new file mode 100644 index 0000000..edd875a --- /dev/null +++ b/space2stats_api/src/space2stats/__main__.py @@ -0,0 +1,23 @@ + +import os + +from .app import app + +try: + import uvicorn # noqa + +except ImportError: # pragma: nocover + uvicorn = None # type: ignore + + +if __name__ == "__main__": + + assert uvicorn is not None, "uvicorn must be installed: `python -m pip install 'space2stats[server]'`" + + uvicorn.run( + app=app, + host=os.getenv("UVICORN_HOST", "127.0.0.1"), + port=os.getenv("UVICORN_PORT", "8000"), + root_path=os.getenv("UVICORN_ROOT_PATH", ""), + log_level="info", + ) diff --git a/space2stats_api/src/space2stats/app.py b/space2stats_api/src/space2stats/app.py new file mode 100644 index 0000000..f60b19f --- /dev/null +++ b/space2stats_api/src/space2stats/app.py @@ -0,0 +1,60 @@ +from contextlib import asynccontextmanager + +from fastapi import FastAPI +from fastapi.middleware.cors import CORSMiddleware +from fastapi.responses import ORJSONResponse + +from typing import Any, Dict, List + +from starlette.requests import Request +from starlette_cramjam.middleware import CompressionMiddleware + +from .db import connect_to_db, close_db_connection +from .main import get_summaries_from_geom, get_available_fields, SummaryRequest + +@asynccontextmanager +async def lifespan(app: FastAPI): + """FastAPI Lifespan.""" + # Create Connection Pool + await connect_to_db(app) + yield + # Close the Connection Pool + await close_db_connection(app) + + +app = FastAPI( + default_response_class=ORJSONResponse, + lifespan=lifespan, +) + +app.add_middleware( + CORSMiddleware, + allow_origins=["*"], + allow_credentials=True, + allow_methods=["*"], + allow_headers=["*"], +) +app.add_middleware(CompressionMiddleware) + + +@app.post("/summary", response_model=List[Dict[str, Any]]) +def get_summary(request: Request, body: SummaryRequest): + with request.app.state.pool.connection() as conn: + return get_summaries_from_geom( + body.aoi, + body.spatial_join_method, + body.fields, + conn, + geometry=body.geometry, + ) + + +@app.get("/fields", response_model=List[str]) +def fields(request: Request): + with request.app.state.pool.connection() as conn: + return get_available_fields(conn) + + +@app.get("/") +def read_root(): + return {"message": "Welcome to Space2Stats!"} diff --git a/space2stats_api/src/space2stats/db.py b/space2stats_api/src/space2stats/db.py new file mode 100644 index 0000000..67ff0a2 --- /dev/null +++ b/space2stats_api/src/space2stats/db.py @@ -0,0 +1,40 @@ +"""Database connection handling.""" + +from typing import Any, Dict, Optional + +from fastapi import FastAPI +from psycopg_pool import ConnectionPool + +from .settings import Settings + + +async def connect_to_db( + app: FastAPI, + settings: Optional[Settings] = None, + pool_kwargs: Optional[Dict[str, Any]] = None, +) -> None: + """Connect to Database.""" + if not settings: + settings = Settings() + + pool_kwargs = pool_kwargs or {} + + app.state.pool = ConnectionPool( + conninfo=settings.DB_CONNECTION_STRING, + min_size=settings.DB_MIN_CONN_SIZE, + max_size=settings.DB_MAX_CONN_SIZE, + max_waiting=settings.DB_MAX_QUERIES, + max_idle=settings.DB_MAX_IDLE, + num_workers=settings.DB_NUM_WORKERS, + kwargs=pool_kwargs, + open=True, + ) + + # Make sure the pool is ready + # ref: https://www.psycopg.org/psycopg3/docs/advanced/pool.html#pool-startup-check + app.state.pool.wait() + + +async def close_db_connection(app: FastAPI) -> None: + """Close Pool.""" + app.state.pool.close() diff --git a/space2stats_api/src/app/utils/h3_utils.py b/space2stats_api/src/space2stats/h3_utils.py similarity index 99% rename from space2stats_api/src/app/utils/h3_utils.py rename to space2stats_api/src/space2stats/h3_utils.py index 9a84e64..7362b80 100644 --- a/space2stats_api/src/app/utils/h3_utils.py +++ b/space2stats_api/src/space2stats/h3_utils.py @@ -35,6 +35,7 @@ def generate_h3_ids( for h3_id in h3_ids if aoi_shape.contains(Polygon(h3.h3_to_geo_boundary(h3_id, geo_json=True))) ] + elif spatial_join_method == "centroid": h3_ids = [ h3_id @@ -73,4 +74,5 @@ def generate_h3_geometries( # h3_to_geo does not have geo_json parameter to invert order of coords x, y = h3.h3_to_geo(h3_id) geometries.append(mapping(Point(y, x))) + return geometries diff --git a/space2stats_api/src/space2stats/handler.py b/space2stats_api/src/space2stats/handler.py new file mode 100644 index 0000000..8884899 --- /dev/null +++ b/space2stats_api/src/space2stats/handler.py @@ -0,0 +1,22 @@ +"""space2stats lambda handler.""" + +import asyncio +import os + +from mangum import Mangum + +from .db import connect_to_db +from .app import app + + +@app.on_event("startup") +async def startup_event() -> None: + """Connect to database on startup.""" + await connect_to_db(app) + + +handler = Mangum(app, lifespan="off") + +if "AWS_EXECUTION_ENV" in os.environ: + loop = asyncio.get_event_loop() + loop.run_until_complete(app.router.startup()) diff --git a/space2stats_api/src/space2stats/main.py b/space2stats_api/src/space2stats/main.py new file mode 100644 index 0000000..93ad60e --- /dev/null +++ b/space2stats_api/src/space2stats/main.py @@ -0,0 +1,139 @@ + + + +from typing import Dict, List, Literal, Optional + +import psycopg as pg +from psycopg import Connection +from pydantic import BaseModel +from geojson_pydantic import Feature, Polygon +from typing_extensions import TypeAlias + +from .h3_utils import generate_h3_ids, generate_h3_geometries +from .settings import Settings + +settings = Settings() + +AoiModel: TypeAlias = Feature[Polygon, Dict] + +class SummaryRequest(BaseModel): + aoi: AoiModel + spatial_join_method: Literal["touches", "centroid", "within"] + fields: List[str] + geometry: Optional[Literal["polygon", "point"]] = None + + +def _get_summaries(fields: List[str], h3_ids: List[str], conn: Connection): + colnames = ["hex_id"] + fields + cols = [pg.sql.Identifier(c) for c in colnames] + sql_query = pg.sql.SQL( + """ + SELECT {0} + FROM {1} + WHERE hex_id = ANY (%s) + """ + ).format(pg.sql.SQL(", ").join(cols), pg.sql.Identifier(settings.DB_TABLE_NAME)) + + # Convert h3_ids to a list to ensure compatibility with psycopg + h3_ids = list(h3_ids) + with conn.cursor() as cur: + cur.execute( + sql_query, + [ + h3_ids, + ], + ) + rows = cur.fetchall() + colnames = [desc[0] for desc in cur.description] + + return rows, colnames + + +def get_summaries_from_geom( + aoi: AoiModel, + spatial_join_method: Literal["touches", "centroid", "within"], + fields: List[str], + conn: Connection, + geometry: Optional[Literal["polygon", "point"]] = None, +): + # Get H3 ids from geometry + resolution = 6 + h3_ids = generate_h3_ids( + aoi.geometry.model_dump(exclude_none=True), + resolution, + spatial_join_method, + ) + + if not h3_ids: + return [] + + # Get Summaries from H3 ids + rows, colnames = _get_summaries(fields, h3_ids, conn) + if not rows: + return [] + + # Format Summaries + summaries: List[Dict] = [] + geometries = ( + generate_h3_geometries(h3_ids, geometry) if geometry else None + ) + + for idx, row in enumerate(rows): + summary = {"hex_id": row[0]} + if geometry and geometries: + summary["geometry"] = geometries[idx] + + summary.update( + { + col: row[idx] + for idx, col in enumerate(colnames[1:], start=1) + if col in fields + } + ) + summaries.append(summary) + + return summaries + + +def get_available_fields(conn: Connection) -> List[str]: + sql_query = """ + SELECT column_name + FROM information_schema.columns + WHERE table_name = %s + """ + with conn.cursor() as cur: + cur.execute( + sql_query, + [ + settings.DB_TABLE_NAME, + ], + ) + columns = [row[0] for row in cur.fetchall() if row[0] != "hex_id"] + + return columns + + +def summaries( + aoi: AoiModel, + spatial_join_method: Literal["touches", "centroid", "within"], + fields: List[str], + geometry: Optional[Literal["polygon", "point"]] = None, +) -> List[Dict]: + """Retrieve Statistics from a GeoJSON feature.""" + if not isinstance(aoi, Feature): + aoi = AoiModel.model_validate(aoi) + + with pg.connect(settings.DB_CONNECTION_STRING) as conn: + return get_summaries_from_geom( + aoi, + spatial_join_method, + fields, + conn, + geometry=geometry, + ) + + +def fields() -> List[str]: + """List Available Fields in the Table.""" + with pg.connect(settings.DB_CONNECTION_STRING) as conn: + return get_available_fields(conn) diff --git a/space2stats_api/src/space2stats/settings.py b/space2stats_api/src/space2stats/settings.py new file mode 100644 index 0000000..4159ad1 --- /dev/null +++ b/space2stats_api/src/space2stats/settings.py @@ -0,0 +1,34 @@ +from pydantic_settings import BaseSettings + + +class Settings(BaseSettings): + DB_HOST: str + DB_PORT: int + DB_NAME: str + DB_USER: str + DB_PASSWORD: str + DB_TABLE_NAME: str + + # see https://www.psycopg.org/psycopg3/docs/api/pool.html#the-connectionpool-class for options + DB_MIN_CONN_SIZE: int = 1 + DB_MAX_CONN_SIZE: int = 10 + + # Maximum number of requests that can be queued to the pool + DB_MAX_QUERIES: int = 50000 + + # Maximum time, in seconds, that a connection can stay unused in the pool before being closed, and the pool shrunk. + DB_MAX_IDLE: float = 300 + + # Number of background worker threads used to maintain the pool state + DB_NUM_WORKERS: int = 3 + + @property + def DB_CONNECTION_STRING(self) -> str: + host_port = f"host={self.DB_HOST} port={self.DB_PORT}" + db_user = f"dbname={self.DB_NAME} user={self.DB_USER}" + return f"{host_port} {db_user} password={self.DB_PASSWORD}" + + model_config = { + "env_file": "local_db.env", + "extra": "ignore", + } diff --git a/space2stats_api/__init__.py b/space2stats_api/src/tests/__init__.py similarity index 100% rename from space2stats_api/__init__.py rename to space2stats_api/src/tests/__init__.py diff --git a/space2stats_api/tests/test_api.py b/space2stats_api/src/tests/test_api.py similarity index 72% rename from space2stats_api/tests/test_api.py rename to space2stats_api/src/tests/test_api.py index baf688c..3d87a2a 100644 --- a/space2stats_api/tests/test_api.py +++ b/space2stats_api/src/tests/test_api.py @@ -1,11 +1,10 @@ from unittest.mock import patch import pytest -from fastapi.testclient import TestClient +from pytest_postgresql.janitor import DatabaseJanitor -from src.app.main import app +from fastapi.testclient import TestClient -client = TestClient(app) aoi = { "type": "Feature", @@ -24,15 +23,43 @@ "properties": {}, } +@pytest.fixture(scope="session") +def database(postgresql_proc): + """Fake Database.""" + with DatabaseJanitor( + user=postgresql_proc.user, + host=postgresql_proc.host, + port=postgresql_proc.port, + dbname="testdb", + version=postgresql_proc.version, + password="password", + ) as jan: + yield jan + + +@pytest.fixture(autouse=True) +def client(monkeypatch, database): + monkeypatch.setenv("DB_HOST", database.host) + monkeypatch.setenv("DB_PORT", str(database.port)) + monkeypatch.setenv("DB_NAME", database.dbname) + monkeypatch.setenv("DB_USER", database.user) + monkeypatch.setenv("DB_PASSWORD", database.password) + monkeypatch.setenv("DB_TABLE_NAME", "space2stats") + + from space2stats.app import app -def test_read_root(): + with TestClient(app) as app: + yield app + + +def test_read_root(client): response = client.get("/") assert response.status_code == 200 assert response.json() == {"message": "Welcome to Space2Stats!"} -@patch("src.app.routers.api.get_summaries") -def test_get_summary(mock_get_summaries): +@patch("space2stats.main._get_summaries") +def test_get_summary(mock_get_summaries, client): mock_get_summaries.return_value = ( [("hex_1", 100, 200)], ["hex_id", "sum_pop_2020", "sum_pop_f_10_2020"] @@ -58,8 +85,8 @@ def test_get_summary(mock_get_summaries): assert len(summary) == len(request_payload["fields"]) + 1 -@patch("src.app.routers.api.get_summaries") -def test_get_summary_with_geometry_polygon(mock_get_summaries): +@patch("space2stats.main._get_summaries") +def test_get_summary_with_geometry_polygon(mock_get_summaries, client): mock_get_summaries.return_value = ( [("hex_1", 100, 200)], ["hex_id", "sum_pop_2020", "sum_pop_f_10_2020"] @@ -88,8 +115,8 @@ def test_get_summary_with_geometry_polygon(mock_get_summaries): assert len(summary) == len(request_payload["fields"]) + 2 -@patch("src.app.routers.api.get_summaries") -def test_get_summary_with_geometry_point(mock_get_summaries): +@patch("space2stats.main._get_summaries") +def test_get_summary_with_geometry_point(mock_get_summaries, client): mock_get_summaries.return_value = ( [("hex_1", 100, 200)], ["hex_id", "sum_pop_2020", "sum_pop_f_10_2020"] @@ -118,8 +145,8 @@ def test_get_summary_with_geometry_point(mock_get_summaries): assert len(summary) == len(request_payload["fields"]) + 2 -@patch("src.app.routers.api.get_available_fields") -def test_get_fields(mock_get_available_fields): +@patch("space2stats.app.get_available_fields") +def test_get_fields(mock_get_available_fields, client): mock_get_available_fields.return_value = ["sum_pop_2020", "sum_pop_f_10_2020", "field3"] @@ -132,7 +159,3 @@ def test_get_fields(mock_get_available_fields): expected_fields = ["sum_pop_2020", "sum_pop_f_10_2020", "field3"] for field in expected_fields: assert field in response_json - - -if __name__ == "__main__": - pytest.main() diff --git a/space2stats_api/tests/test_h3_utils.py b/space2stats_api/src/tests/test_h3_utils.py similarity index 96% rename from space2stats_api/tests/test_h3_utils.py rename to space2stats_api/src/tests/test_h3_utils.py index 222f035..b7b8082 100644 --- a/space2stats_api/tests/test_h3_utils.py +++ b/space2stats_api/src/tests/test_h3_utils.py @@ -1,7 +1,7 @@ import pytest from shapely.geometry import Polygon, mapping -from src.app.utils.h3_utils import generate_h3_geometries, generate_h3_ids +from space2stats.h3_utils import generate_h3_geometries, generate_h3_ids polygon_coords = [ [-74.3, 40.5], diff --git a/space2stats_api/tests/__init__.py b/space2stats_api/tests/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/space2stats_api/tests/test_db_utils.py b/space2stats_api/tests/test_db_utils.py deleted file mode 100644 index 222f035..0000000 --- a/space2stats_api/tests/test_db_utils.py +++ /dev/null @@ -1,68 +0,0 @@ -import pytest -from shapely.geometry import Polygon, mapping - -from src.app.utils.h3_utils import generate_h3_geometries, generate_h3_ids - -polygon_coords = [ - [-74.3, 40.5], - [-73.7, 40.5], - [-73.7, 40.9], - [-74.3, 40.9], - [-74.3, 40.5], -] -polygon = Polygon(polygon_coords) -aoi_geojson = mapping(polygon) -resolution = 6 - - -def test_generate_h3_ids_within(): - h3_ids = generate_h3_ids(aoi_geojson, resolution, "within") - print(f"Test 'within' - Generated H3 IDs: {h3_ids}") - assert len(h3_ids) > 0, "Expected at least one H3 ID" - - -def test_generate_h3_ids_touches(): - h3_ids = generate_h3_ids(aoi_geojson, resolution, "touches") - print(f"Test 'touches' - Generated H3 IDs: {h3_ids}") - assert len(h3_ids) > 0, "Expected at least one H3 ID" - - -def test_generate_h3_ids_centroid(): - h3_ids = generate_h3_ids(aoi_geojson, resolution, "centroid") - print(f"Test 'centroid' - Generated H3 IDs: {h3_ids}") - assert len(h3_ids) > 0, "Expected at least one H3 ID for centroid" - - -def test_generate_h3_ids_invalid_method(): - with pytest.raises(ValueError, match="Invalid spatial join method"): - generate_h3_ids(aoi_geojson, resolution, "invalid_method") - - -def test_generate_h3_geometries_polygon(): - h3_ids = generate_h3_ids(aoi_geojson, resolution, "touches") - geometries = generate_h3_geometries(h3_ids, "polygon") - assert len(geometries) == len( - h3_ids - ), "Expected the same number of geometries as H3 IDs" - for geom in geometries: - assert geom["type"] == "Polygon", "Expected Polygon geometry" - - -def test_generate_h3_geometries_point(): - h3_ids = generate_h3_ids(aoi_geojson, resolution, "touches") - geometries = generate_h3_geometries(h3_ids, "point") - assert len(geometries) == len( - h3_ids - ), "Expected the same number of geometries as H3 IDs" - for geom in geometries: - assert geom["type"] == "Point", "Expected Point geometry" - - -def test_generate_h3_geometries_invalid_type(): - h3_ids = generate_h3_ids(aoi_geojson, resolution, "touches") - with pytest.raises(ValueError, match="Invalid geometry type"): - generate_h3_geometries(h3_ids, "invalid_type") - - -if __name__ == "__main__": - pytest.main()