Ensure special keys are not in content when loaded (#112)

* Ensure special keys not in content when loaded

The loader pop'd keys like collection off the item, then dehydrated the
item to be used as the 'content'. With collection removed prior to
dehydration, it was flagged with the "do-not-merge" marker because the
key is on the base_item. Instead, ensure that id, collection, and
geometry are not in content as they are stored on the table row and
shouldn't participate in hydration.

Additionally, bbox was previously a derived value at search runtime but
was recently changed to a returned value if it existed on the item.
However, during loading, the bbox was dropped so would never exist on
the persisted item.

* Simplify geometry check

pypgstac/pypgstac/load.py

@@ -511,8 +511,8 @@ def format_item(self, _item: Union[Path, str, dict]) -> dict:
 
         base_item, key, partition_trunc = self.collection_json(item["collection"])
 
-        out["id"] = item.pop("id")
-        out["collection"] = item.pop("collection")
+        out["id"] = item.get("id")
+        out["collection"] = item.get("collection")
         properties: dict = item.get("properties", {})
 
         dt = properties.get("datetime")
@@ -544,16 +544,21 @@ def format_item(self, _item: Union[Path, str, dict]) -> dict:
 
         out["partition"] = partition
 
-        bbox = item.pop("bbox")
-        geojson = item.pop("geometry")
-        if geojson is None and bbox is not None:
+        geojson = item.get("geometry")
+        if geojson is None:
             geometry = None
         else:
             geometry = str(Geometry.from_geojson(geojson).wkb)
         out["geometry"] = geometry
 
         content = dehydrate(base_item, item)
 
+        # Remove keys from the dehydrated item content which are stored directly
+        # on the table row.
+        content.pop("id", None)
+        content.pop("collection", None)
+        content.pop("geometry", None)
+
         out["content"] = orjson.dumps(content).decode()
 
         return out

pypgstac/tests/test_load.py

@@ -1,6 +1,7 @@
 """Tests for pypgstac."""
+import json
 from pathlib import Path
-from pypgstac.load import Methods, Loader
+from pypgstac.load import Methods, Loader, read_json
 from psycopg.errors import UniqueViolation
 import pytest
 
@@ -239,3 +240,30 @@ def test_load_items_dehydrated_ignore_succeeds(loader: Loader) -> None:
     loader.load_items(
         str(TEST_DEHYDRATED_ITEMS), insert_mode=Methods.ignore, dehydrated=True
     )
+
+
+def test_format_items_keys(loader: Loader) -> None:
+    """Test pypgstac items ignore loader."""
+    loader.load_collections(
+        str(TEST_COLLECTIONS_JSON),
+        insert_mode=Methods.ignore,
+    )
+
+    items_iter = read_json(str(TEST_ITEMS))
+    item_json = next(iter(items_iter))
+    out = loader.format_item(item_json)
+
+    # Top level keys expected after format
+    assert "id" in out
+    assert "collection" in out
+    assert "geometry" in out
+    assert "content" in out
+
+    # Special keys expected not to be in the item content
+    content_json = json.loads(out["content"])
+    assert "id" not in content_json
+    assert "collection" not in content_json
+    assert "geometry" not in content_json
+
+    # Ensure bbox is included in content
+    assert "bbox" in content_json