Merge branch 'main' into add-opensearch

Author: jamesfisher-geo

CHANGELOG.md

@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### Changed
 
 - Elasticsearch drivers from 7.17.9 to 8.11.0 [#169](https://github.com/stac-utils/stac-fastapi-elasticsearch/pull/169)
+- Collection update endpoint no longer delete all sub items [#177](https://github.com/stac-utils/stac-fastapi-elasticsearch/pull/177)
 
 ### Fixed
 

docker-compose.yml

@@ -14,7 +14,7 @@ services:
       - RELOAD=true
       - ENVIRONMENT=local
       - WEB_CONCURRENCY=10
-      - ES_HOST=172.17.0.1
+      - ES_HOST=elasticsearch
       - ES_PORT=9200
       - ES_USE_SSL=false
       - ES_VERIFY_CERTS=false
@@ -62,6 +62,7 @@ services:
   elasticsearch:
     container_name: es-container
     image: docker.elastic.co/elasticsearch/elasticsearch:${ELASTICSEARCH_VERSION:-8.11.0}
+    hostname: elasticsearch
     environment:
       ES_JAVA_OPTS: -Xms512m -Xmx1g
     volumes:

stac_fastapi/elasticsearch/stac_fastapi/elasticsearch/config/config_elasticsearch.py

@@ -39,6 +39,15 @@ def _es_config() -> Dict[str, Any]:
     if (u := os.getenv("ES_USER")) and (p := os.getenv("ES_PASS")):
         config["http_auth"] = (u, p)
 
+    if api_key := os.getenv("ES_API_KEY"):
+        if isinstance(config["headers"], dict):
+            headers = {**config["headers"], "x-api-key": api_key}
+
+        else:
+            config["headers"] = {"x-api-key": api_key}
+
+        config["headers"] = headers
+
     return config
 
 

stac_fastapi/elasticsearch/stac_fastapi/elasticsearch/core.py

@@ -468,9 +468,9 @@ async def post_search(
             )
 
         if search_request.query:
-            for (field_name, expr) in search_request.query.items():
+            for field_name, expr in search_request.query.items():
                 field = "properties__" + field_name
-                for (op, value) in expr.items():
+                for op, value in expr.items():
                     search = self.database.apply_stacql_filter(
                         search=search, op=op, field=field, value=value
                     )
@@ -671,8 +671,11 @@ async def update_collection(
         Update a collection.
 
         This method updates an existing collection in the database by first finding
-        the collection by its id, then deleting the old version, and finally creating
-        a new version of the updated collection. The updated collection is then returned.
+        the collection by the id given in the keyword argument `collection_id`.
+        If no `collection_id` is given the id of the given collection object is used.
+        If the object and keyword collection ids don't match the sub items
+        collection id is updated else the items are left unchanged.
+        The updated collection is then returned.
 
         Args:
             collection: A STAC collection that needs to be updated.
@@ -684,9 +687,18 @@ async def update_collection(
         """
         base_url = str(kwargs["request"].base_url)
 
-        await self.database.find_collection(collection_id=collection["id"])
-        await self.delete_collection(collection["id"])
-        await self.create_collection(collection, **kwargs)
+        collection_id = kwargs["request"].query_params.get(
+            "collection_id", collection["id"]
+        )
+
+        collection_links = CollectionLinks(
+            collection_id=collection["id"], base_url=base_url
+        ).create_links()
+        collection["links"] = collection_links
+
+        await self.database.update_collection(
+            collection_id=collection_id, collection=collection
+        )
 
         return CollectionSerializer.db_to_stac(collection, base_url)
 

stac_fastapi/elasticsearch/stac_fastapi/elasticsearch/database_logic/database_logic_elasticsearch.py

@@ -749,6 +749,53 @@ async def find_collection(self, collection_id: str) -> Collection:
 
         return collection["_source"]
 
+    async def update_collection(
+        self, collection_id: str, collection: Collection, refresh: bool = False
+    ):
+        """Update a collection from the database.
+
+        Args:
+            self: The instance of the object calling this function.
+            collection_id (str): The ID of the collection to be updated.
+            collection (Collection): The Collection object to be used for the update.
+
+        Raises:
+            NotFoundError: If the collection with the given `collection_id` is not
+            found in the database.
+
+        Notes:
+            This function updates the collection in the database using the specified
+            `collection_id` and with the collection specified in the `Collection` object.
+            If the collection is not found, a `NotFoundError` is raised.
+        """
+        await self.find_collection(collection_id=collection_id)
+
+        if collection_id != collection["id"]:
+            await self.create_collection(collection, refresh=refresh)
+
+            await self.client.reindex(
+                body={
+                    "dest": {"index": f"{ITEMS_INDEX_PREFIX}{collection['id']}"},
+                    "source": {"index": f"{ITEMS_INDEX_PREFIX}{collection_id}"},
+                    "script": {
+                        "lang": "painless",
+                        "source": f"""ctx._id = ctx._id.replace('{collection_id}', '{collection["id"]}'); ctx._source.collection = '{collection["id"]}' ;""",
+                    },
+                },
+                wait_for_completion=True,
+                refresh=refresh,
+            )
+
+            await self.delete_collection(collection_id)
+
+        else:
+            await self.client.index(
+                index=COLLECTIONS_INDEX,
+                id=collection_id,
+                document=collection,
+                refresh=refresh,
+            )
+
     async def delete_collection(self, collection_id: str, refresh: bool = False):
         """Delete a collection from the database.
 

stac_fastapi/elasticsearch/tests/clients/test_elasticsearch.py

@@ -40,16 +40,90 @@ async def test_update_collection(
     txn_client,
     load_test_data: Callable,
 ):
-    data = load_test_data("test_collection.json")
+    collection_data = load_test_data("test_collection.json")
+    item_data = load_test_data("test_item.json")
 
-    await txn_client.create_collection(data, request=MockRequest)
-    data["keywords"].append("new keyword")
-    await txn_client.update_collection(data, request=MockRequest)
+    await txn_client.create_collection(collection_data, request=MockRequest)
+    await txn_client.create_item(
+        collection_id=collection_data["id"],
+        item=item_data,
+        request=MockRequest,
+        refresh=True,
+    )
 
-    coll = await core_client.get_collection(data["id"], request=MockRequest)
+    collection_data["keywords"].append("new keyword")
+    await txn_client.update_collection(collection_data, request=MockRequest)
+
+    coll = await core_client.get_collection(collection_data["id"], request=MockRequest)
     assert "new keyword" in coll["keywords"]
 
-    await txn_client.delete_collection(data["id"])
+    item = await core_client.get_item(
+        item_id=item_data["id"],
+        collection_id=collection_data["id"],
+        request=MockRequest,
+    )
+    assert item["id"] == item_data["id"]
+    assert item["collection"] == item_data["collection"]
+
+    await txn_client.delete_collection(collection_data["id"])
+
+
+@pytest.mark.asyncio
+async def test_update_collection_id(
+    core_client,
+    txn_client,
+    load_test_data: Callable,
+):
+    collection_data = load_test_data("test_collection.json")
+    item_data = load_test_data("test_item.json")
+    new_collection_id = "new-test-collection"
+
+    await txn_client.create_collection(collection_data, request=MockRequest)
+    await txn_client.create_item(
+        collection_id=collection_data["id"],
+        item=item_data,
+        request=MockRequest,
+        refresh=True,
+    )
+
+    old_collection_id = collection_data["id"]
+    collection_data["id"] = new_collection_id
+
+    await txn_client.update_collection(
+        collection=collection_data,
+        request=MockRequest(
+            query_params={
+                "collection_id": old_collection_id,
+                "limit": "10",
+            }
+        ),
+        refresh=True,
+    )
+
+    with pytest.raises(NotFoundError):
+        await core_client.get_collection(old_collection_id, request=MockRequest)
+
+    coll = await core_client.get_collection(collection_data["id"], request=MockRequest)
+    assert coll["id"] == new_collection_id
+
+    with pytest.raises(NotFoundError):
+        await core_client.get_item(
+            item_id=item_data["id"],
+            collection_id=old_collection_id,
+            request=MockRequest,
+        )
+
+    item = await core_client.get_item(
+        item_id=item_data["id"],
+        collection_id=collection_data["id"],
+        request=MockRequest,
+        refresh=True,
+    )
+
+    assert item["id"] == item_data["id"]
+    assert item["collection"] == new_collection_id
+
+    await txn_client.delete_collection(collection_data["id"])
 
 
 @pytest.mark.asyncio

stac_fastapi/elasticsearch/tests/conftest.py

@@ -51,6 +51,7 @@ def __init__(self, item, collection):
 
 class MockRequest:
     base_url = "http://test-server"
+    query_params = {}
 
     def __init__(
         self,
@@ -62,7 +63,7 @@ def __init__(
         self.method = method
         self.url = url
         self.app = app
-        self.query_params = query_params or {}
+        self.query_params = query_params
 
 
 class TestSettings(AsyncSearchSettings):