Updated stac-fastapi-sqlachemy to work with pydantic v2, stacapi v6.0.0

.gitignore

@@ -1,5 +1,5 @@
 .mypy_cache
-
+env2/
 PIP_EXTRA_INDEX_URL
 !tests/resources/*.jpg
 **.pyc
@@ -131,4 +131,4 @@ docs/api/*
 venv
 
 # IDE
-.vscode
+.vscode

CHANGES.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## Updated
+
+* Api functionality updated to work with stacapi v6.0.0 release
+
+
 ## [Unreleased]
 
 As a part of this release, this repository was extracted from the main

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.8-slim as base
+FROM python:3.13-slim as base
 
 # Any python libraries that require system libraries to be installed will likely
 # need the following packages in order to build
@@ -16,4 +16,5 @@ WORKDIR /app
 
 COPY . /app
 
+RUN pip install pip --upgrade
 RUN pip install -e .[dev,server]

Dockerfile.docs

@@ -1,10 +1,10 @@
-FROM python:3.8-slim
+FROM python:3.11-slim
 
 # build-essential is required to build a wheel for ciso8601
 RUN apt update && apt install -y build-essential
 
 RUN python -m pip install --upgrade pip
-RUN python -m pip install mkdocs mkdocs-material pdocs
+RUN python -m pip install "numpy<2" mkdocs mkdocs-material pdocs pystac
 
 COPY . /opt/src
 

docker-compose.docs.yml

@@ -1,5 +1,3 @@
-version: '3'
-
 services:
   docs:
     container_name: stac-fastapi-docs-dev

docker-compose.nginx.yml

@@ -1,4 +1,3 @@
-version: '3'
 services:
   nginx:
     image: nginx

docker-compose.yml

@@ -1,4 +1,3 @@
-version: '3'
 services:
   app:
     container_name: stac-fastapi-sqlalchemy
@@ -22,6 +21,8 @@ services:
     volumes:
       - ./stac_fastapi:/app/stac_fastapi
       - ./scripts:/app/scripts
+      - ./tests:/app/tests
+      - ./test_data:/app/test_data
     depends_on:
       - database
     command: bash -c "./scripts/wait-for-it.sh database:5432 && python -m stac_fastapi.sqlalchemy.app"

setup.py

@@ -7,18 +7,19 @@
 
 install_requires = [
     "attrs",
-    "pydantic[dotenv]",
-    "stac_pydantic>=2.0.3",
-    "stac-fastapi.types",
-    "stac-fastapi.api",
-    "stac-fastapi.extensions",
+    "pydantic",
+    "stac_pydantic",
+    "stac-fastapi.types==6.0.0",
+    "stac-fastapi.api==6.0.0",
+    "stac-fastapi.extensions==6.0.0",
     "sqlakeyset",
-    "geoalchemy2<0.14.0",
+    "geoalchemy2",
     "sqlalchemy==1.3.23",
     "shapely",
     "psycopg2-binary",
     "alembic",
     "fastapi-utils",
+    "typing-inspect",
 ]
 
 extra_reqs = {
@@ -34,7 +35,7 @@
         "wheel",
     ],
     "docs": ["mkdocs", "mkdocs-material", "pdocs"],
-    "server": ["uvicorn[standard]==0.19.0"],
+    "server": ["uvicorn[standard]==0.35.0"],
 }
 
 
@@ -48,7 +49,7 @@
         "Intended Audience :: Developers",
         "Intended Audience :: Information Technology",
         "Intended Audience :: Science/Research",
-        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.13",
         "License :: OSI Approved :: MIT License",
     ],
     keywords="STAC FastAPI COG",

stac_fastapi/sqlalchemy/app.py

@@ -4,7 +4,7 @@
 from stac_fastapi.api.app import StacApi
 from stac_fastapi.api.models import create_get_request_model, create_post_request_model
 from stac_fastapi.extensions.core import (
-    ContextExtension,
+    #ContextExtension,
     FieldsExtension,
     SortExtension,
     TokenPaginationExtension,
@@ -30,7 +30,7 @@
     QueryExtension(),
     SortExtension(),
     TokenPaginationExtension(),
-    ContextExtension(),
+    #ContextExtension(),
 ]
 
 post_request_model = create_post_request_model(extensions)
@@ -39,11 +39,12 @@
     settings=settings,
     extensions=extensions,
     client=CoreCrudClient(
-        session=session, extensions=extensions, post_request_model=post_request_model
+        session=session, extensions=extensions , post_request_model=post_request_model
     ),
     search_get_request_model=create_get_request_model(extensions),
     search_post_request_model=post_request_model,
 )
+
 app = api.app
 
 

stac_fastapi/sqlalchemy/core.py

@@ -17,6 +17,7 @@
 from sqlakeyset import get_page
 from sqlalchemy import func
 from sqlalchemy.orm import Session as SqlSession
+from stac_fastapi.api.models import create_post_request_model
 from stac_fastapi.types.config import Settings
 from stac_fastapi.types.core import BaseCoreClient
 from stac_fastapi.types.errors import NotFoundError
@@ -50,6 +51,12 @@ class CoreCrudClient(PaginationTokenClient, BaseCoreClient):
         default=serializers.CollectionSerializer
     )
 
+    #added attribute post_request_model to the class core crud client
+    post_request_model: type = attr.ib(factory=lambda: create_post_request_model([]))
+
+
+
+
     @staticmethod
     def _lookup_id(
         id: str, table: Type[database.BaseModel], session: SqlSession
@@ -129,7 +136,16 @@ def item_collection(
                     bbox_2d = [bbox[0], bbox[1], bbox[3], bbox[4]]
                     geom = ShapelyPolygon.from_bounds(*bbox_2d)
             if geom:
-                filter_geom = ga.shape.from_shape(geom, srid=4326)
+                # Ensure `geom` is a Shapely geometry
+                if not hasattr(geom, "wkt"):
+                    geom = shape(geom)
+
+                #convert to WKT
+                wkt = geom.wkt  
+
+                """use shapelys shape method, geoalchemy's shape attribute has been removed""" 
+                filter_geom = func.ST_GeomFromText(wkt, 4326)
+                #filter_geom = from_shape(geom, srid=4326)
                 query = query.filter(
                     ga.func.ST_Intersects(self.item_table.geometry, filter_geom)
                 )
@@ -262,9 +278,10 @@ def get_search(
             "bbox": bbox,
             "limit": limit,
             "token": token,
+            "fields": fields,
             "query": json.loads(unquote_plus(query)) if query else query,
         }
-
+        #print(f"\n--------------------------------Parsed base_args---------------\n\n{base_args}")
         if datetime:
             base_args["datetime"] = datetime
 
@@ -294,13 +311,16 @@ def get_search(
                 else:
                     includes.add(field)
             base_args["fields"] = {"include": includes, "exclude": excludes}
+            #print(f'-----------------------base args: {base_args["fields"]}--------------------------')
 
         # Do the request
         try:
             search_request = self.post_request_model(**base_args)
+            #print(f"\n------------------------------Validated search_request------\n\n", search_request)
         except ValidationError:
             raise HTTPException(status_code=400, detail="Invalid parameters provided")
         resp = self.post_search(search_request, request=kwargs["request"])
+        #print(f'\n------------------search response before pagination links----------------------\n\n{resp}\n\n{type(resp)}')
 
         # Pagination
         page_links = []
@@ -317,6 +337,7 @@ def get_search(
             else:
                 page_links.append(link)
         resp["links"] = page_links
+
         return resp
 
     def post_search(
@@ -397,12 +418,26 @@ def post_search(
                         ]
                         geom = ShapelyPolygon.from_bounds(*bbox_2d)
 
+                # if geom:
+                #     filter_geom = ga.shape(geom, srid=4326)
+                #     query = query.filter(
+                #         ga.func.ST_Intersects(self.item_table.geometry, filter_geom)
+                #     )
+                """geoalchemy has removed the shape attribute, we default to shapely"""
                 if geom:
-                    filter_geom = ga.shape.from_shape(geom, srid=4326)
+                    # Ensure `geom` is a Shapely geometry
+                    if not hasattr(geom, "wkt"):
+                        geom = shape(geom)
+
+                    # Convert to WKT
+                    wkt = geom.wkt  
+
+                    filter_geom = func.ST_GeomFromText(wkt, 4326)
                     query = query.filter(
-                        ga.func.ST_Intersects(self.item_table.geometry, filter_geom)
+                        func.ST_Intersects(self.item_table.geometry, filter_geom)
                     )
 
+
                 # Temporal query
                 if search_request.datetime:
                     # Two tailed query (between)
@@ -481,9 +516,16 @@ def post_search(
                 response_features.append(
                     self.item_serializer.db_to_stac(item, base_url=base_url)
                 )
+            #for i in response_features:
+                ##print(f'----------------response item(db_to_stac) --------------\n\n{i}')
 
-            # Use pydantic includes/excludes syntax to implement fields extension
+            #apply the fields extension logic
             if self.extension_is_enabled("FieldsExtension"):
+
+                include = getattr(search_request.fields, "include", set()) or set()
+                exclude = getattr(search_request.fields, "exclude", set()) or set()
+
+                #dynamically include query fields
                 if search_request.query is not None:
                     query_include: Set[str] = set(
                         [
@@ -493,18 +535,26 @@ def post_search(
                             for k in search_request.query.keys()
                         ]
                     )
-                    if not search_request.fields.include:
-                        search_request.fields.include = query_include
-                    else:
-                        search_request.fields.include.union(query_include)
-
-                filter_kwargs = search_request.fields.filter_fields
-                # Need to pass through `.json()` for proper serialization
-                # of datetime
-                response_features = [
-                    json.loads(stac_pydantic.Item(**feat).json(**filter_kwargs))
-                    for feat in response_features
-                ]
+
+                # Only pass if non-empty
+                if include and len(include) > 0:
+                    response_features = [
+                        json.loads(stac_pydantic.Item(**feat).model_dump_json(include=include))
+                        for feat in response_features
+                    ]
+                    #print(f'---------------------------------fields extension response included------------------------\n\n{response_features}')
+                elif exclude and len(exclude) > 0:
+                    response_features = [
+                        json.loads(stac_pydantic.Item(**feat).model_dump_json(exclude=exclude))
+                        for feat in response_features
+                    ]
+                    #print(f'---------------------------------fields extension response excluded------------------------\n\n{response_features}')
+
+                else:
+                    response_features = [
+                        json.loads(stac_pydantic.Item(**feat).model_dump_json())
+                        for feat in response_features
+                    ]
 
         context_obj = None
         if self.extension_is_enabled("ContextExtension"):
@@ -519,4 +569,4 @@ def post_search(
             features=response_features,
             links=links,
             context=context_obj,
-        )
+        )

stac_fastapi/sqlalchemy/extensions/query.py

@@ -11,11 +11,11 @@
 from typing import Any, Callable, Dict, Optional, Union
 
 import sqlalchemy as sa
-from pydantic import BaseModel, ValidationError, root_validator
-from pydantic.error_wrappers import ErrorWrapper
+from pydantic import BaseModel, ValidationError, root_validator, model_validator
+#from pydantic.error_wrappers import ErrorWrapper
 from stac_fastapi.extensions.core.query import QueryExtension as QueryExtensionBase
 from stac_pydantic.utils import AutoValueEnum
-
+from stac_fastapi.types.search import BaseSearchPostRequest
 logger = logging.getLogger("uvicorn")
 logger.setLevel(logging.INFO)
 # Be careful: https://github.com/samuelcolvin/pydantic/issues/1423#issuecomment-642797287
@@ -99,10 +99,11 @@ class QueryExtensionPostRequest(BaseModel):
     Add queryables validation to the POST request
     to raise errors for unsupported querys.
     """
+    #added `= None` to make it fully optional
+    query: Optional[Dict[Queryables, Dict[Operator, Any]]] = None
 
-    query: Optional[Dict[Queryables, Dict[Operator, Any]]]
-
-    @root_validator(pre=True)
+    @model_validator(mode="before")
+    #@root_validator(pre=True)
     def validate_query_fields(cls, values: Dict) -> Dict:
         """Validate query fields."""
         logger.debug(f"Validating SQLAlchemySTACSearch {cls} {values}")
@@ -112,10 +113,10 @@ def validate_query_fields(cls, values: Dict) -> Dict:
                 if field_name not in queryable_fields:
                     raise ValidationError(
                         [
-                            ErrorWrapper(
-                                ValueError(f"Cannot search on field: {field_name}"),
-                                "STACSearch",
-                            )
+                            {
+                                'loc': ('query', field_name), 
+                                'msg': f"Cannot search on field: {field_name}", 'type': 'value_error'
+                            }
                         ],
                         QueryExtensionPostRequest,
                     )