def get_database_model(cls, schema: schemas.Item) -> dict:
"""Decompose pydantic model to data model."""
indexed_fields = {}
for field in Settings.get().indexed_fields:
# Use getattr to accommodate extension namespaces
field_value = getattr(schema.properties, field)
if field == "datetime":
field_value = datetime.strptime(field_value, DATETIME_RFC339)
indexed_fields[field.split(":")[-1]] = field_value
# Exclude indexed fields from the properties jsonb field
properties = schema.properties.dict(
exclude=set(Settings.get().indexed_fields))
now = datetime.utcnow().strftime(DATETIME_RFC339)
if not properties["created"]:
properties["created"] = now
properties["updated"] = now
return dict(
collection_id=schema.collection,
geometry=ga.shape.from_shape(shape(schema.geometry), 4326),
properties=properties,
**indexed_fields,
**schema.dict(
exclude_none=True,
exclude=set(Settings().get().forbidden_fields
| {"geometry", "properties", "collection"}),
))
def __attrs_post_init__(self):
"""Post-init hook.
Responsible for setting up the application upon instantiation of the class.
Returns:
None
"""
# inject settings
self.client.extensions = self.extensions
fields_ext = self.get_extension(FieldsExtension)
if fields_ext:
self.settings.default_includes = fields_ext.default_includes
Settings.set(self.settings)
self.register_core()
# register extensions
for ext in self.extensions:
ext.register(self.app)
# add health check
self.add_health_check()
# register exception handlers
add_exception_handlers(self.app, status_codes=self.exceptions)
# customize openapi
self.app.openapi = self.customize_openapi
def __init__(self, obj: Any):
"""Decompose orm model to pydantic model."""
properties = obj.properties.copy()
for field in Settings.get().indexed_fields:
# Use getattr to accommodate extension namespaces
field_value = getattr(obj, field.split(":")[-1])
if field == "datetime":
field_value = field_value.strftime(DATETIME_RFC339)
properties[field] = field_value
# Create inferred links
item_links = ItemLinks(
collection_id=obj.collection_id, base_url=obj.base_url, item_id=obj.id
).create_links()
# Resolve existing links
if obj.links:
item_links += resolve_links(obj.links, obj.base_url)
db_model = obj.__class__(
id=obj.id,
stac_version=obj.stac_version,
geometry=self.decode_geom(obj.geometry),
bbox=obj.bbox,
properties=properties,
assets=obj.assets,
collection_id=obj.collection_id,
datetime=obj.datetime,
links=item_links,
stac_extensions=obj.stac_extensions,
)
db_model.type = "Feature"
db_model.collection = db_model.collection_id
super().__init__(db_model)
def stac_to_db(cls,
stac_data: TypedDict,
exclude_geometry: bool = False) -> database.Item:
"""Transform stac item to database model."""
indexed_fields = {}
for field in Settings.get().indexed_fields:
# Use getattr to accommodate extension namespaces
field_value = stac_data["properties"][field]
if field == "datetime":
field_value = datetime.strptime(field_value, DATETIME_RFC339)
indexed_fields[field.split(":")[-1]] = field_value
# TODO: Exclude indexed fields from the properties jsonb field to prevent duplication
now = datetime.utcnow().strftime(DATETIME_RFC339)
if "created" not in stac_data["properties"]:
stac_data["properties"]["created"] = now
stac_data["properties"]["updated"] = now
return database.Item(
id=stac_data["id"],
collection_id=stac_data["collection"],
stac_version=stac_data["stac_version"],
stac_extensions=stac_data.get("stac_extensions"),
geometry=json.dumps(stac_data["geometry"]),
bbox=stac_data["bbox"],
properties=stac_data["properties"],
assets=stac_data["assets"],
**indexed_fields,
)
def __attrs_post_init__(self):
"""Post-init hook.
Responsible for setting up the application upon instantiation of the class.
Returns:
None
"""
# inject settings
self.client.extensions = self.extensions
self.client.stac_version = self.stac_version
self.client.title = self.title
self.client.description = self.description
fields_ext = self.get_extension(FieldsExtension)
if fields_ext:
self.settings.default_includes = fields_ext.default_includes
Settings.set(self.settings)
self.app.state.settings = self.settings
# Register core STAC endpoints
self.register_core()
self.app.include_router(self.router)
# register extensions
for ext in self.extensions:
ext.register(self.app)
# add health check
self.add_health_check()
# register exception handlers
add_exception_handlers(self.app, status_codes=self.exceptions)
# customize openapi
self.app.openapi = self.customize_openapi
# add middlewares
for middleware in self.middlewares:
self.app.add_middleware(middleware)
def filter_fields(self) -> Dict:
"""Create pydantic include/exclude expression.
Create dictionary of fields to include/exclude on model export based on the included and excluded fields passed
to the API
Ref: https://pydantic-docs.helpmanual.io/usage/exporting_models/#advanced-include-and-exclude
"""
# Always include default_includes, even if they
# exist in the exclude list.
include = (self.include or set()) - (self.exclude or set())
include |= Settings.get().default_includes or set()
return {
"include": self._get_field_dict(include),
"exclude": self._get_field_dict(self.exclude),
}
def db_to_stac(cls, db_model: database.Item,
base_url: str) -> stac_types.Item:
"""Transform database model to stac item."""
properties = db_model.properties.copy()
indexed_fields = Settings.get().indexed_fields
for field in indexed_fields:
# Use getattr to accommodate extension namespaces
field_value = getattr(db_model, field.split(":")[-1])
if field == "datetime":
field_value = field_value.strftime(DATETIME_RFC339)
properties[field] = field_value
item_id = db_model.id
collection_id = db_model.collection_id
item_links = ItemLinks(collection_id=collection_id,
item_id=item_id,
base_url=base_url).create_links()
db_links = db_model.links
if db_links:
item_links += resolve_links(db_links, base_url)
stac_extensions = db_model.stac_extensions or []
# The custom geometry we are using emits geojson if the geometry is bound to the database
# Otherwise it will return a geoalchemy2 WKBElement
# TODO: It's probably best to just remove the custom geometry type
geometry = db_model.geometry
if isinstance(geometry, ga.elements.WKBElement):
geometry = ga.shape.to_shape(geometry).__geo_interface__
if isinstance(geometry, str):
geometry = json.loads(geometry)
return stac_types.Item(
type="Feature",
stac_version=db_model.stac_version,
stac_extensions=stac_extensions,
id=db_model.id,
collection=db_model.collection_id,
geometry=geometry,
bbox=[float(x) for x in db_model.bbox],
properties=properties,
links=item_links,
assets=db_model.assets,
)
def post_search(self, search_request: STACSearch,
**kwargs) -> Dict[str, Any]:
"""POST search catalog."""
with self.session.reader.context_session() as session:
token = (self.get_token(search_request.token)
if search_request.token else False)
query = session.query(self.item_table)
# Filter by collection
count = None
if search_request.collections:
query = query.join(self.collection_table).filter(
sa.or_(*[
self.collection_table.id == col_id
for col_id in search_request.collections
]))
# Sort
if search_request.sortby:
sort_fields = [
getattr(self.item_table.get_field(sort.field),
sort.direction.value)()
for sort in search_request.sortby
]
sort_fields.append(self.item_table.id)
query = query.order_by(*sort_fields)
else:
# Default sort is date
query = query.order_by(self.item_table.datetime.desc(),
self.item_table.id)
# Ignore other parameters if ID is present
if search_request.ids:
id_filter = sa.or_(
*[self.item_table.id == i for i in search_request.ids])
items = query.filter(id_filter).order_by(self.item_table.id)
page = get_page(items,
per_page=search_request.limit,
page=token)
if self.extension_is_enabled(ContextExtension):
count = len(search_request.ids)
page.next = (self.insert_token(
keyset=page.paging.bookmark_next)
if page.paging.has_next else None)
page.previous = (self.insert_token(
keyset=page.paging.bookmark_previous)
if page.paging.has_previous else None)
else:
# Spatial query
poly = None
if search_request.intersects is not None:
poly = shape(search_request.intersects)
elif search_request.bbox:
poly = ShapelyPolygon.from_bounds(*search_request.bbox)
if poly:
filter_geom = ga.shape.from_shape(poly, srid=4326)
query = query.filter(
ga.func.ST_Intersects(self.item_table.geometry,
filter_geom))
# Temporal query
if search_request.datetime:
# Two tailed query (between)
if ".." not in search_request.datetime:
query = query.filter(
self.item_table.datetime.between(
*search_request.datetime))
# All items after the start date
if search_request.datetime[0] != "..":
query = query.filter(self.item_table.datetime >=
search_request.datetime[0])
# All items before the end date
if search_request.datetime[1] != "..":
query = query.filter(self.item_table.datetime <=
search_request.datetime[1])
# Query fields
if search_request.query:
for (field_name, expr) in search_request.query.items():
field = self.item_table.get_field(field_name)
for (op, value) in expr.items():
query = query.filter(op.operator(field, value))
if self.extension_is_enabled(ContextExtension):
count_query = query.statement.with_only_columns(
[func.count()]).order_by(None)
count = query.session.execute(count_query).scalar()
page = get_page(query,
per_page=search_request.limit,
page=token)
# Create dynamic attributes for each page
page.next = (self.insert_token(
keyset=page.paging.bookmark_next)
if page.paging.has_next else None)
page.previous = (self.insert_token(
keyset=page.paging.bookmark_previous)
if page.paging.has_previous else None)
links = []
if page.next:
links.append(
PaginationLink(
rel=Relations.next,
type="application/geo+json",
href=f"{kwargs['request'].base_url}search",
method="POST",
body={"token": page.next},
merge=True,
))
if page.previous:
links.append(
PaginationLink(
rel=Relations.previous,
type="application/geo+json",
href=f"{kwargs['request'].base_url}search",
method="POST",
body={"token": page.previous},
merge=True,
))
response_features = []
filter_kwargs = {}
if self.extension_is_enabled(FieldsExtension):
if search_request.query is not None:
query_include: Set[str] = set([
k if k in Settings.get().indexed_fields else
f"properties.{k}" for k in search_request.query.keys()
])
if not search_request.field.include:
search_request.field.include = query_include
else:
search_request.field.include.union(query_include)
filter_kwargs = search_request.field.filter_fields
xvals = []
yvals = []
for item in page:
item.base_url = str(kwargs["request"].base_url)
item_model = schemas.Item.from_orm(item)
xvals += [item_model.bbox[0], item_model.bbox[2]]
yvals += [item_model.bbox[1], item_model.bbox[3]]
response_features.append(item_model.to_dict(**filter_kwargs))
try:
bbox = (min(xvals), min(yvals), max(xvals), max(yvals))
except ValueError:
bbox = None
context_obj = None
if self.extension_is_enabled(ContextExtension):
context_obj = {
"returned": len(page),
"limit": search_request.limit,
"matched": count,
}
return {
"type": "FeatureCollection",
"context": context_obj,
"features": response_features,
"links": links,
"bbox": bbox,
}
def post_search(self, search_request: SQLAlchemySTACSearch,
**kwargs) -> ItemCollection:
"""POST search catalog."""
base_url = str(kwargs["request"].base_url)
with self.session.reader.context_session() as session:
token = (self.get_token(search_request.token)
if search_request.token else False)
query = session.query(self.item_table)
# Filter by collection
count = None
if search_request.collections:
query = query.join(self.collection_table).filter(
sa.or_(*[
self.collection_table.id == col_id
for col_id in search_request.collections
]))
# Sort
if search_request.sortby:
sort_fields = [
getattr(
self.item_table.get_field(sort.field),
sort.direction.value,
)() for sort in search_request.sortby
]
sort_fields.append(self.item_table.id)
query = query.order_by(*sort_fields)
else:
# Default sort is date
query = query.order_by(self.item_table.datetime.desc(),
self.item_table.id)
# Ignore other parameters if ID is present
if search_request.ids:
id_filter = sa.or_(
*[self.item_table.id == i for i in search_request.ids])
items = query.filter(id_filter).order_by(self.item_table.id)
page = get_page(items,
per_page=search_request.limit,
page=token)
if self.extension_is_enabled(ContextExtension):
count = len(search_request.ids)
page.next = (self.insert_token(
keyset=page.paging.bookmark_next)
if page.paging.has_next else None)
page.previous = (self.insert_token(
keyset=page.paging.bookmark_previous)
if page.paging.has_previous else None)
else:
# Spatial query
poly = None
if search_request.intersects is not None:
poly = shape(search_request.intersects)
elif search_request.bbox:
poly = ShapelyPolygon.from_bounds(*search_request.bbox)
if poly:
filter_geom = ga.shape.from_shape(poly, srid=4326)
query = query.filter(
ga.func.ST_Intersects(self.item_table.geometry,
filter_geom))
# Temporal query
if search_request.datetime:
# Two tailed query (between)
dts = search_request.datetime.split("/")
if ".." not in search_request.datetime:
query = query.filter(
self.item_table.datetime.between(*dts))
# All items after the start date
if dts[0] != "..":
query = query.filter(
self.item_table.datetime >= dts[0])
# All items before the end date
if dts[1] != "..":
query = query.filter(
self.item_table.datetime <= dts[1])
# Query fields
if search_request.query:
for (field_name, expr) in search_request.query.items():
field = self.item_table.get_field(field_name)
for (op, value) in expr.items():
query = query.filter(op.operator(field, value))
if self.extension_is_enabled(ContextExtension):
count_query = query.statement.with_only_columns(
[func.count()]).order_by(None)
count = query.session.execute(count_query).scalar()
page = get_page(query,
per_page=search_request.limit,
page=token)
# Create dynamic attributes for each page
page.next = (self.insert_token(
keyset=page.paging.bookmark_next)
if page.paging.has_next else None)
page.previous = (self.insert_token(
keyset=page.paging.bookmark_previous)
if page.paging.has_previous else None)
links = []
if page.next:
links.append({
"rel": Relations.next.value,
"type": "application/geo+json",
"href": f"{kwargs['request'].base_url}search",
"method": "POST",
"body": {
"token": page.next
},
"merge": True,
})
if page.previous:
links.append({
"rel": Relations.previous.value,
"type": "application/geo+json",
"href": f"{kwargs['request'].base_url}search",
"method": "POST",
"body": {
"token": page.previous
},
"merge": True,
})
response_features = []
for item in page:
response_features.append(
self.item_serializer.db_to_stac(item, base_url=base_url))
# Use pydantic includes/excludes syntax to implement fields extension
if self.extension_is_enabled(FieldsExtension):
if search_request.query is not None:
query_include: Set[str] = set([
k if k in Settings.get().indexed_fields else
f"properties.{k}" for k in search_request.query.keys()
])
if not search_request.field.include:
search_request.field.include = query_include
else:
search_request.field.include.union(query_include)
filter_kwargs = search_request.field.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
]
context_obj = None
if self.extension_is_enabled(ContextExtension):
context_obj = {
"returned": len(page),
"limit": search_request.limit,
"matched": count,
}
# TODO: return stac_extensions
return ItemCollection(
type="FeatureCollection",
stac_version=STAC_VERSION,
features=response_features,
links=links,
context=context_obj,
)
BulkTransactionsClient,
TransactionsClient,
)
from stac_fastapi.sqlalchemy.types.search import SQLAlchemySTACSearch
from stac_fastapi.types.config import Settings
DATA_DIR = os.path.join(os.path.dirname(__file__), "data")
class TestSettings(SqlalchemySettings):
class Config:
env_file = ".env.test"
settings = TestSettings()
Settings.set(settings)
@pytest.fixture(autouse=True)
def cleanup(postgres_core: CoreCrudClient,
postgres_transactions: TransactionsClient):
yield
collections = postgres_core.all_collections(request=MockStarletteRequest)
for coll in collections:
if coll.id.split("-")[0] == "test":
# Delete the items
items = postgres_core.item_collection(coll.id,
limit=100,
request=MockStarletteRequest)
for feat in items.features:
postgres_transactions.delete_item(feat.id,
