Make item geometry and bbox nullable for sqlalchemy backend (#398)

Closes #350
stac-utils · Jul 13, 2022 · 0e4fea3 · 0e4fea3
1 parent 52438a1
commit 0e4fea3
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diff --git a/CHANGES.md b/CHANGES.md
@@ -19,6 +19,7 @@
   ([#355](https://github.com/stac-utils/stac-fastapi/issues/355))
 * docker-compose now runs uvicorn with hot-reloading enabled
 * Bump version of PGStac to 0.6.2 that includes support for hydrating results in the API backed ([#397](https://github.com/stac-utils/stac-fastapi/pull/397))
+* Make item geometry and bbox nullable in sqlalchemy backend. ([#398](https://github.com/stac-utils/stac-fastapi/pull/398))
 
 ### Removed
 

diff --git a/..._fastapi/sqlalchemy/alembic/versions/7016c1bf3fbf_make_item_geometry_and_bbox_nullable.py b/..._fastapi/sqlalchemy/alembic/versions/7016c1bf3fbf_make_item_geometry_and_bbox_nullable.py
@@ -0,0 +1,46 @@
+"""Make item geometry and bbox nullable
+
+Revision ID: 7016c1bf3fbf
+Revises: 5909bd10f2e6
+Create Date: 2022-04-28 10:40:06.856826
+
+"""
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "7016c1bf3fbf"
+down_revision = "5909bd10f2e6"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.alter_column(
+        schema="data",
+        table_name="items",
+        column_name="geometry",
+        nullable=True,
+    )
+    op.alter_column(
+        schema="data",
+        table_name="items",
+        column_name="bbox",
+        nullable=True,
+    )
+
+
+def downgrade():
+    # Downgrading will require the user to update or remove all null geometry
+    # cases from the DB, otherwise the downgrade migration will fail.
+    op.alter_column(
+        schema="data",
+        table_name="items",
+        column_name="geometry",
+        nullable=False,
+    )
+    op.alter_column(
+        schema="data",
+        table_name="items",
+        column_name="bbox",
+        nullable=False,
+    )
diff --git a/stac_fastapi/sqlalchemy/setup.py b/stac_fastapi/sqlalchemy/setup.py
@@ -8,7 +8,7 @@
 install_requires = [
     "attrs",
     "pydantic[dotenv]",
-    "stac_pydantic==2.0.*",
+    "stac_pydantic>=2.0.3",
     "stac-fastapi.types",
     "stac-fastapi.api",
     "stac-fastapi.extensions",

diff --git a/stac_fastapi/sqlalchemy/stac_fastapi/sqlalchemy/models/database.py b/stac_fastapi/sqlalchemy/stac_fastapi/sqlalchemy/models/database.py
@@ -64,8 +64,10 @@ class Item(BaseModel):  # type:ignore
     id = sa.Column(sa.VARCHAR(1024), nullable=False, primary_key=True)
     stac_version = sa.Column(sa.VARCHAR(300))
     stac_extensions = sa.Column(sa.ARRAY(sa.VARCHAR(300)), nullable=True)
-    geometry = sa.Column(GeojsonGeometry("GEOMETRY", srid=4326, spatial_index=True))
-    bbox = sa.Column(sa.ARRAY(sa.NUMERIC), nullable=False)
+    geometry = sa.Column(
+        GeojsonGeometry("GEOMETRY", srid=4326, spatial_index=True), nullable=True
+    )
+    bbox = sa.Column(sa.ARRAY(sa.NUMERIC), nullable=True)
     properties = sa.Column(JSONB)
     assets = sa.Column(JSONB)
     collection_id = sa.Column(

diff --git a/stac_fastapi/sqlalchemy/stac_fastapi/sqlalchemy/serializers.py b/stac_fastapi/sqlalchemy/stac_fastapi/sqlalchemy/serializers.py
@@ -78,14 +78,18 @@ def db_to_stac(cls, db_model: database.Item, base_url: str) -> stac_types.Item:
         if isinstance(geometry, str):
             geometry = json.loads(geometry)
 
+        bbox = db_model.bbox
+        if bbox is not None:
+            bbox = [float(x) for x in db_model.bbox]
+
         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],
+            bbox=bbox,
             properties=properties,
             links=item_links,
             assets=db_model.assets,
@@ -111,13 +115,17 @@ def stac_to_db(
                 stac_data["properties"]["created"] = now
             stac_data["properties"]["updated"] = now
 
+        geometry = stac_data["geometry"]
+        if geometry is not None:
+            geometry = json.dumps(geometry)
+
         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"],
+            geometry=geometry,
+            bbox=stac_data.get("bbox"),
             properties=stac_data["properties"],
             assets=stac_data["assets"],
             **indexed_fields,

diff --git a/stac_fastapi/sqlalchemy/tests/api/test_api.py b/stac_fastapi/sqlalchemy/tests/api/test_api.py
@@ -92,6 +92,21 @@ def test_app_search_response_multipolygon(
     assert resp_json.get("features")[0]["geometry"]["type"] == "MultiPolygon"
 
 
+def test_app_search_response_geometry_null(
+    load_test_data, app_client, postgres_transactions
+):
+    item = load_test_data("test_item_geometry_null.json")
+    postgres_transactions.create_item(item, request=MockStarletteRequest)
+
+    resp = app_client.get("/search", params={"collections": ["test-collection"]})
+    assert resp.status_code == 200
+    resp_json = resp.json()
+
+    assert resp_json.get("type") == "FeatureCollection"
+    assert resp_json.get("features")[0]["geometry"] is None
+    assert resp_json.get("features")[0]["bbox"] is None
+
+
 def test_app_context_extension(load_test_data, app_client, postgres_transactions):
     item = load_test_data("test_item.json")
     postgres_transactions.create_item(item, request=MockStarletteRequest)

diff --git a/stac_fastapi/sqlalchemy/tests/data/test_item_geometry_null.json b/stac_fastapi/sqlalchemy/tests/data/test_item_geometry_null.json
@@ -0,0 +1,169 @@
+{
+    "type": "Feature",
+    "stac_version": "1.0.0",
+    "stac_extensions": [
+      "https://landsat.usgs.gov/stac/landsat-ard-extension/v1.0.0/schema.json",
+      "https://stac-extensions.github.io/projection/v1.0.0/schema.json",
+      "https://stac-extensions.github.io/eo/v1.0.0/schema.json",
+      "https://stac-extensions.github.io/alternate-assets/v1.1.0/schema.json",
+      "https://stac-extensions.github.io/storage/v1.0.0/schema.json"
+    ],
+    "id": "LE07_CU_002012_20150101_20210502_02_BA",
+    "description": "Landsat Collection 2 Level-3 Burned Area Product",
+    "geometry": null,
+    "properties": {
+      "datetime": "2015-01-01T18:39:12.4885358Z",
+      "platform": "LANDSAT_7",
+      "instruments": [
+        "ETM"
+      ],
+      "landsat:grid_horizontal": "02",
+      "landsat:grid_vertical": "12",
+      "landsat:grid_region": "CU",
+      "landsat:scene_count": 1,
+      "eo:cloud_cover": 0.0759,
+      "landsat:cloud_shadow_cover": 0.1394,
+      "landsat:snow_ice_cover": 0,
+      "landsat:fill": 95.4286,
+      "proj:epsg": null,
+      "proj:shape": [
+        5000,
+        5000
+      ],
+      "proj:transform": [
+        30,
+        0,
+        -2265585,
+        0,
+        -30,
+        1514805
+      ],
+      "created": "2022-02-08T20:07:38.885Z",
+      "updated": "2022-02-08T20:07:38.885Z"
+    },
+    "assets": {
+      "index": {
+        "title": "HTML index page",
+        "type": "text/html",
+        "roles": [
+          "metadata"
+        ],
+        "href": "https://landsatlook.usgs.gov/stac-browser/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02"
+      },
+      "bp": {
+        "title": "Burn Probability",
+        "description": "Collection 2 Level-3 Albers Burn Probability Burned Area",
+        "type": "image/vnd.stac.geotiff; cloud-optimized=true",
+        "roles": [
+          "data"
+        ],
+        "href": "https://landsatlook.usgs.gov/level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02_BP.TIF",
+        "alternate": {
+          "s3": {
+            "storage:platform": "AWS",
+            "storage:requester_pays": true,
+            "href": "s3://usgs-landsat-level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02_BP.TIF"
+          }
+        }
+      },
+      "bc": {
+        "title": "Burn Classification",
+        "description": "Collection 2 Level-3 Albers Burn Classification Burned Area",
+        "type": "image/vnd.stac.geotiff; cloud-optimized=true",
+        "roles": [
+          "data"
+        ],
+        "href": "https://landsatlook.usgs.gov/level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02_BC.TIF",
+        "alternate": {
+          "s3": {
+            "storage:platform": "AWS",
+            "storage:requester_pays": true,
+            "href": "s3://usgs-landsat-level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02_BC.TIF"
+          }
+        }
+      },
+      "quick_look": {
+        "title": "Quick Look File",
+        "description": "Collection 2 Level-3 Albers Quick Look File Burned Area",
+        "type": "image/png",
+        "roles": [
+          "data"
+        ],
+        "href": "https://landsatlook.usgs.gov/level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02_QuickLook.png",
+        "alternate": {
+          "s3": {
+            "storage:platform": "AWS",
+            "storage:requester_pays": true,
+            "href": "s3://usgs-landsat-level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02_QuickLook.png"
+          }
+        }
+      },
+      "xml": {
+        "title": "Extensible Metadata File",
+        "description": "Collection 2 Level-3 Albers Extensible Metadata File Burned Area",
+        "type": "application/xml",
+        "roles": [
+          "metadata"
+        ],
+        "href": "https://landsatlook.usgs.gov/level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02.xml",
+        "alternate": {
+          "s3": {
+            "storage:platform": "AWS",
+            "storage:requester_pays": true,
+            "href": "s3://usgs-landsat-level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02.xml"
+          }
+        }
+      },
+      "json": {
+        "title": "Extensible Metadata File (json)",
+        "description": "Collection 2 Level-3 Albers Extensible Metadata File (json) Burned Area",
+        "type": "application/json",
+        "roles": [
+          "metadata"
+        ],
+        "href": "https://landsatlook.usgs.gov/level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02.json",
+        "alternate": {
+          "s3": {
+            "storage:platform": "AWS",
+            "storage:requester_pays": true,
+            "href": "s3://usgs-landsat-level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02.json"
+          }
+        }
+      }
+    },
+    "links": [
+      {
+        "rel": "self",
+        "href": "https://landsatlook.usgs.gov/stac-server/collections/landsat-c2l3-ba/items/LE07_CU_002012_20150101_20210502_02_BA"
+      },
+      {
+        "rel": "derived_from",
+        "href": "https://landsatlook.usgs.gov/stac-server/collections/landsat-c2ard-sr/items/LE07_CU_002012_20150101_20210502_02_SR"
+      },
+      {
+        "rel": "derived_from",
+        "href": "https://landsatlook.usgs.gov/stac-server/collections/landsat-c2ard-st/items/LE07_CU_002012_20150101_20210502_02_ST"
+      },
+      {
+        "rel": "derived_from",
+        "href": "https://landsatlook.usgs.gov/stac-server/collections/landsat-c2ard-ta/items/LE07_CU_002012_20150101_20210502_02_TOA"
+      },
+      {
+        "rel": "derived_from",
+        "href": "https://landsatlook.usgs.gov/stac-server/collections/landsat-c2ard-bt/items/LE07_CU_002012_20150101_20210502_02_BT"
+      },
+      {
+        "rel": "parent",
+        "href": "https://landsatlook.usgs.gov/stac-server/collections/landsat-c2l3-ba"
+      },
+      {
+        "rel": "collection",
+        "href": "https://landsatlook.usgs.gov/stac-server/collections/landsat-c2l3-ba"
+      },
+      {
+        "rel": "root",
+        "href": "https://landsatlook.usgs.gov/stac-server/"
+      }
+    ],
+    "collection": "test-collection"
+  }