Fix/python deps

README.md

@@ -164,7 +164,7 @@ As an example, below we update the backend on a development machine:
 
 ```bash
 # Edit docker-compose-prod-build.yaml image version:
-#     image: ghcr.io/nismod/gri-backend:1.5.0
+#     image: ghcr.io/nismod/gri-backend:1.6.2
 
 # Build
 docker compose -f docker-compose-prod-build.yaml build backend
@@ -173,17 +173,17 @@ docker compose -f docker-compose-prod-build.yaml build backend
 # see: https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry
 
 # Push
-docker push ghcr.io/nismod/gri-backend:1.5.0
+docker push ghcr.io/nismod/gri-backend:1.6.2
 ```
 
 On the production remote, pull the image and restart the service:
 
 ```bash
 # Pull image
-docker pull ghcr.io/nismod/gri-backend:1.5.0
+docker pull ghcr.io/nismod/gri-backend:1.6.2
 
 # Edit docker-compose-prod-deploy.yaml image version (or sync up):
-#     image: ghcr.io/nismod/gri-backend:1.5.0
+#     image: ghcr.io/nismod/gri-backend:1.6.2
 
 # Restart service
 docker compose up -d backend

containers/backend/Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.10
+FROM python:3.12
 LABEL maintainer="frederick.thomas@ouce.ox.ac.uk"
 
 WORKDIR /code

containers/backend/README.md

@@ -30,7 +30,7 @@ source venv/bin/activate
 pip install -e .[dev]
 
 # run the application
-uvicorn app.main:app --port 8888 --reload
+uvicorn backend.app.main:app --port 8888 --reload
 ```
 
 ## Configuration

containers/backend/backend/app/dependencies.py

@@ -1,4 +1,4 @@
-from db.database import SessionLocal
+from backend.db.database import SessionLocal
 
 
 def get_db():

containers/backend/backend/app/internal/attribute_access.py

@@ -7,8 +7,8 @@
 from pydantic import Json, ValidationError
 
 
-from app import schemas
-from db import models
+from backend.app import schemas
+from backend.db import models
 
 
 def add_damages_expected_value_query(
@@ -55,7 +55,7 @@ def add_adaptation_value_query(
         adaptation_protection_level=dimensions.adaptation_protection_level,
     )
 
-    value: Column | ColumnOperators = None
+    value: Column | ColumnOperators | None = None
 
     if field == "cost_benefit_ratio":
         cost_benefit_params: schemas.AdaptationCostBenefitRatioParameters = field_params
@@ -78,7 +78,7 @@ class DataGroupConfig:
     add_value_query: Callable[
         [Query, schemas.DataDimensions, str, schemas.DataParameters | None], Query
     ]
-    field_parameters_schemas: Optional[dict[str, schemas.DataParameters]] = None
+    field_parameters_schemas: Optional[dict[str, schemas.DataParameters]] | None = None
 
 
 DATA_GROUP_CONFIGS: dict[str, DataGroupConfig] = {

containers/backend/backend/app/internal/helpers.py

@@ -5,7 +5,7 @@
 import logging
 import traceback
 
-from config import TILEDB_URI
+from backend.config import TILEDB_URI
 
 
 def build_driver_path(database: str, tiledb_uri: str = TILEDB_URI) -> str:

containers/backend/backend/app/main.py

@@ -4,8 +4,11 @@
 from fastapi.routing import APIRoute
 from fastapi.logger import logger
 
-from .routers import attributes, features, tiles, colormap
-from config import LOG_LEVEL
+import backend.app.routers.attributes as attributes
+import backend.app.routers.features as features
+import backend.app.routers.tiles as tiles
+import backend.app.routers.colormap as colormap
+from backend.config import LOG_LEVEL
 
 formatter = logging.Formatter(
     "[%(asctime)s.%(msecs)03d] %(levelname)s %(filename)s - %(funcName)s - %(message)s",

containers/backend/backend/app/routers/attributes.py

@@ -2,16 +2,16 @@
 from fastapi import APIRouter, Body, Depends
 from sqlalchemy.orm import Session
 
-from app.dependencies import get_db
-from app.internal.attribute_access import (
+from backend.app.dependencies import get_db
+from backend.app.internal.attribute_access import (
     add_value_query,
     parse_dimensions,
     parse_parameters,
 )
 
-from db import models
+from backend.db import models
 
-from .. import schemas
+from backend.app import schemas
 
 router = APIRouter(tags=["attributes"])
 

containers/backend/backend/app/routers/colormap.py

@@ -4,13 +4,12 @@
 
 import inspect
 import json
-from typing import Union
 
 from fastapi import APIRouter, HTTPException
 from fastapi.logger import logger
 
-from app import schemas
-from app.internal.helpers import handle_exception
+from backend.app import schemas
+from backend.app.internal.helpers import handle_exception
 
 
 router = APIRouter(tags=["colormap"])
@@ -29,7 +28,7 @@ def _get_colormap(options: schemas.ColorMapOptions) -> schemas.ColorMap:
 @router.get("", response_model=schemas.ColorMap)
 async def get_colormap(
     colormap: str,
-    stretch_range: Union[str, None],
+    stretch_range: str,
     num_values: int = 255,
 ) -> schemas.ColorMap:
     """
@@ -43,18 +42,28 @@ async def get_colormap(
 
     ::kwarg num_values int Number of values to generate in the colormap
     """
+    try:
+        stretch_range_arg: list[int] = json.loads(stretch_range)
+        if len(stretch_range_arg) != 2:
+            raise ValueError
+    except ValueError:
+        raise HTTPException(
+            status_code=400,
+            detail="stretch_range should be a list of two values (min and max), like `stretch_range=[0,1]`",
+        )
+
     logger.debug(
         "performing %s, using %s, %s, %s",
         inspect.stack()[0][3],
         colormap,
-        json.loads(stretch_range),
+        stretch_range_arg,
         num_values,
     )
     try:
 
         options = schemas.ColorMapOptions(
             colormap=colormap,
-            stretch_range=json.loads(stretch_range),
+            stretch_range=stretch_range_arg,
             num_values=num_values,
         )
 

containers/backend/backend/app/routers/features.py

@@ -1,3 +1,5 @@
+from typing import Optional
+
 from fastapi import APIRouter, Depends, HTTPException
 from fastapi_pagination import Page, Params
 from fastapi_pagination.ext.sqlalchemy import paginate
@@ -6,14 +8,14 @@
 from sqlalchemy.orm import Session
 from geoalchemy2 import functions
 
-from app import schemas
-from app.dependencies import get_db
-from app.internal.attribute_access import (
+from backend.app import schemas
+from backend.app.dependencies import get_db
+from backend.app.internal.attribute_access import (
     add_value_query,
     parse_dimensions,
     parse_parameters,
 )
-from db import models
+from backend.db import models
 
 
 router = APIRouter(tags=["features"])
@@ -32,7 +34,10 @@ def read_feature(feature_id: int, db: Session = Depends(get_db)):
 
 
 def get_layer_spec(
-    layer: str = None, sector: str = None, subsector: str = None, asset_type: str = None
+    layer: Optional[str] = None,
+    sector: Optional[str] = None,
+    subsector: Optional[str] = None,
+    asset_type: Optional[str] = None,
 ):
     return schemas.LayerSpec(
         layer_name=layer,

containers/backend/backend/app/routers/tiles.py

@@ -17,15 +17,15 @@
 from terracotta import get_driver
 
 
-from app import schemas
-from app.dependencies import get_db
-from db import models
-from app.internal.helpers import build_driver_path, handle_exception
-from app.exceptions import (
+from backend.app import schemas
+from backend.app.dependencies import get_db
+from backend.db import models
+from backend.app.internal.helpers import build_driver_path, handle_exception
+from backend.app.exceptions import (
     SourceDBDoesNotExistException,
     MissingExplicitColourMapException,
 )
-from config import CATEGORICAL_COLOR_MAPS
+from backend.config import CATEGORICAL_COLOR_MAPS
 
 
 router = APIRouter(tags=["tiles"])

containers/backend/backend/app/schemas.py

@@ -1,6 +1,7 @@
 from enum import Enum
-from typing import Generic, List, Optional, TypeVar, Union
-from pydantic import BaseModel, ConfigDict, conint, validator
+from typing import Generic, Optional, TypeVar, Union
+from typing_extensions import Annotated
+from pydantic import BaseModel, ConfigDict, Field, field_validator
 
 
 class FeatureBase(BaseModel):
@@ -113,9 +114,9 @@ class AdaptationVariables(DataVariables):
 
 
 class AdaptationCostBenefitRatioParameters(DataParameters):
-    eael_days: conint(ge=1, le=30)
+    eael_days: Annotated[int, Field(ge=1, le=30)]
 
-    @validator("eael_days")
+    @field_validator("eael_days")
     def fix_eael_days(cls, eael_days: int) -> float:
         """
         The data for `AdaptationCostBenefit.avoided_eael_mean` is erroneous and
@@ -187,19 +188,19 @@ class TileSourceMeta(BaseModel):
 
 
 class TileSourceDomains(BaseModel):
-    domains: List[dict[str, str]]
+    domains: list[dict[str, str]]
 
 
 class ColorMapOptions(BaseModel):
-    stretch_range: List[int]
+    stretch_range: list[int]
     colormap: str
     num_values: Optional[int] = 255
 
 
 class ColorMapEntry(BaseModel):
     value: float
-    rgba: List[int]
+    rgba: list[int]
 
 
 class ColorMap(BaseModel):
-    colormap: List[ColorMapEntry]
+    colormap: list[ColorMapEntry]

containers/backend/backend/create_schema.py

@@ -2,8 +2,8 @@
 SQLAlchemy Schema Setup Main
 """
 
-from db import models
-from db.database import engine
+from backend.db import models
+from backend.db.database import engine
 
 if __name__ == "__main__":
     models.Base.metadata.drop_all(bind=engine)

containers/backend/pyproject.toml

@@ -4,20 +4,22 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gri-backend"
-version = "0.3.0"
+version = "0.4.1"
 description = "GRI API Backend"
 readme = "README.md"
-requires-python = ">=3.7"
+requires-python = ">=3.12"
 license = { text = "MIT" }
 classifiers = ["Framework :: FastAPI", "Programming Language :: Python :: 3"]
 dependencies = [
-    "fastapi==0.109.1",
-    "geoalchemy2==0.12.5",
-    "uvicorn==0.18.3",
+    "fastapi==0.115.5",
+    "fastapi-pagination==0.12.32",
+    "geoalchemy2==0.16.0",
     "psycopg2-binary==2.9.10",
-    "fastapi-pagination==0.10.0",
+    "pydantic==2.9.2",
+    "sqlalchemy==2.0.36",
+    "setuptools==75.5.0",
     "terracotta==0.8.3",
-    "sqlalchemy==1.4.41",
+    "uvicorn==0.32.0",
 ]
 
 [project.optional-dependencies]

docker-compose-dev.yaml

@@ -45,7 +45,7 @@ services:
 
   backend:
     build: ./containers/backend
-    image: ghcr.io/nismod/gri-backend:1.5.0
+    image: ghcr.io/nismod/gri-backend:1.6.2
     volumes:
       - ./etl/raster/cog/:/data/
       - ./containers/backend/backend/:/code/backend/
@@ -118,7 +118,7 @@ services:
   ## WARNING - this will wipe the existing tables. TODO: Alembic
   recreate-metadata-schema:
     build: ./containers/backend
-    image: ghcr.io/nismod/gri-backend:1.5.0
+    image: ghcr.io/nismod/gri-backend:1.6.2
     profiles: ["recreate-metadata-schema"]
     volumes:
       - ./containers/backend/backend/db/models.py:/code/backend/db/models.py

docker-compose-prod-build.yaml

@@ -1,6 +1,6 @@
 services:
   backend:
-    image: ghcr.io/nismod/gri-backend:1.5.0
+    image: ghcr.io/nismod/gri-backend:1.6.2
     build: ./containers/backend
 
   vector-tileserver:

docker-compose-prod-deploy.yaml

@@ -45,7 +45,7 @@ services:
     mem_limit: "250M"
 
   backend:
-    image: ghcr.io/nismod/gri-backend:1.5.0
+    image: ghcr.io/nismod/gri-backend:1.6.2
     restart: always
     volumes:
       - ./tileserver/raster/data:/data