Stop using S3 Select in indexer (#4212)

Co-authored-by: Alexei Mochalov <[email protected]>

lambdas/indexer/CHANGELOG.md

@@ -0,0 +1,21 @@
+<!-- markdownlint-disable line-length -->
+# Changelog
+
+Changes are listed in reverse chronological order (newer entries at the top).
+The entry format is
+
+```markdown
+- [Verb] Change description ([#<PR-number>](https://github.com/quiltdata/quilt/pull/<PR-number>))
+```
+
+where verb is one of
+
+- Removed
+- Added
+- Fixed
+- Changed
+
+## Changes
+
+- [Changed] Stop using S3 select ([#4212](https://github.com/quiltdata/quilt/pull/4212))
+- [Added] Bootstrap the change log ([#4212](https://github.com/quiltdata/quilt/pull/4212))

lambdas/indexer/index.py

@@ -47,6 +47,7 @@
 
 
 import datetime
+import functools
 import json
 import os
 import pathlib
@@ -92,7 +93,6 @@
     POINTER_PREFIX_V1,
     get_available_memory,
     get_quilt_logger,
-    query_manifest_content,
     separated_env_to_iter,
 )
 
@@ -168,12 +168,7 @@
 # currently only affects .parquet, TODO: extend to other extensions
 assert 'SKIP_ROWS_EXTS' in os.environ
 SKIP_ROWS_EXTS = separated_env_to_iter('SKIP_ROWS_EXTS')
-SELECT_PACKAGE_META = "SELECT * from S3Object o WHERE o.version IS NOT MISSING LIMIT 1"
-# No WHERE clause needed for aggregations since S3 Select skips missing fields for aggs
-SELECT_PACKAGE_STATS = (
-    "SELECT COALESCE(SUM(obj['size']), 0) as total_bytes,"
-    " COUNT(obj['size']) as total_files from S3Object obj"
-)
+DUCKDB_SELECT_LAMBDA_ARN = os.environ["DUCKDB_SELECT_LAMBDA_ARN"]
 TEST_EVENT = "s3:TestEvent"
 # we need to filter out GetObject and HeadObject calls generated by the present
 #  lambda in order to display accurate analytics in the Quilt catalog
@@ -182,6 +177,7 @@
 
 
 logger = get_quilt_logger()
+s3_client = boto3.client("s3", config=botocore.config.Config(user_agent_extra=USER_AGENT_EXTRA))
 
 
 def now_like_boto3():
@@ -247,13 +243,10 @@ def select_manifest_meta(s3_client, bucket: str, key: str):
     wrapper for retry and returning a string
     """
     try:
-        raw = query_manifest_content(
-            s3_client,
-            bucket=bucket,
-            key=key,
-            sql_stmt=SELECT_PACKAGE_META
-        )
-        return json.load(raw)
+        body = s3_client.get_object(Bucket=bucket, Key=key)["Body"]
+        with body:  # this *might* be needed to close the stream ASAP
+            for line in body.iter_lines():
+                return json.loads(line)
     except (botocore.exceptions.ClientError, json.JSONDecodeError) as cle:
         print(f"Unable to S3 select manifest: {cle}")
 
@@ -439,7 +432,7 @@ def get_pkg_data():
         first = select_manifest_meta(s3_client, bucket, manifest_key)
         if not first:
             return
-        stats = select_package_stats(s3_client, bucket, manifest_key)
+        stats = select_package_stats(bucket, manifest_key)
         if not stats:
             return
 
@@ -472,33 +465,54 @@ def get_pkg_data():
     return True
 
 
-def select_package_stats(s3_client, bucket, manifest_key) -> str:
+@functools.lru_cache(maxsize=None)
+def get_bucket_region(bucket: str) -> str:
+    resp = s3_client.head_bucket(Bucket=bucket)
+    return resp["ResponseMetadata"]["HTTPHeaders"]["x-amz-bucket-region"]
+
+
+@functools.lru_cache(maxsize=None)
+def get_presigner_client(bucket: str):
+    return boto3.client(
+        "s3",
+        region_name=get_bucket_region(bucket),
+        config=botocore.config.Config(signature_version="s3v4"),
+    )
+
+
+def select_package_stats(bucket, manifest_key) -> Optional[dict]:
     """use s3 select to generate file stats for package"""
     logger_ = get_quilt_logger()
-    try:
-        raw_stats = query_manifest_content(
-            s3_client,
-            bucket=bucket,
-            key=manifest_key,
-            sql_stmt=SELECT_PACKAGE_STATS
-        ).read()
-
-        if raw_stats:
-            stats = json.loads(raw_stats)
-            assert isinstance(stats['total_bytes'], int)
-            assert isinstance(stats['total_files'], int)
-
-            return stats
-
-    except (
-            AssertionError,
-            botocore.exceptions.ClientError,
-            json.JSONDecodeError,
-            KeyError,
-    ) as err:
-        logger_.exception("Unable to compute package stats via S3 select")
+    presigner_client = get_presigner_client(bucket)
+    url = presigner_client.generate_presigned_url(
+        ClientMethod="get_object",
+        Params={
+            "Bucket": bucket,
+            "Key": manifest_key,
+        },
+    )
+    lambda_ = make_lambda_client()
+    q = f"""
+    SELECT
+        COALESCE(SUM(size), 0) AS total_bytes,
+        COUNT(size) AS total_files FROM read_ndjson('{url}', columns={{size: 'UBIGINT'}}) obj
+    """
+    resp = lambda_.invoke(
+        FunctionName=DUCKDB_SELECT_LAMBDA_ARN,
+        Payload=json.dumps({"query": q, "user_agent": f"DuckDB Select {USER_AGENT_EXTRA}"}),
+    )
 
-    return None
+    payload = resp["Payload"].read()
+    if "FunctionError" in resp:
+        logger_.error("DuckDB select unhandled error: %s", payload)
+        return None
+    parsed = json.loads(payload)
+    if "error" in parsed:
+        logger_.error("DuckDB select error: %s", parsed["error"])
+        return None
+
+    rows = parsed["rows"]
+    return rows[0] if rows else None
 
 
 def extract_pptx(fileobj, max_size: int) -> str:
@@ -732,6 +746,11 @@ def make_s3_client():
     return boto3.client("s3", config=configuration)
 
 
+@functools.lru_cache(maxsize=None)
+def make_lambda_client():
+    return boto3.client("lambda")
+
+
 def map_event_name(event: dict):
     """transform eventbridge names into S3-like ones"""
     input_ = event["eventName"]

lambdas/indexer/pytest.ini

@@ -1,4 +1,6 @@
 [pytest]
+env =
+    DUCKDB_SELECT_LAMBDA_ARN = "arn:aws:lambda:us-west-2:123456789012:function:select-lambda"
 log_cli = True
 # This is set above critical to prevent logger events from confusing output in CI
-log_level = 51 
+log_level = 51

lambdas/indexer/test-requirements.txt

@@ -5,4 +5,5 @@ pluggy==0.9
 py==1.10.0
 pytest==4.4.0
 pytest-cov==2.6.1
+pytest-env==0.6.2
 responses==0.10.14

lambdas/indexer/test/test_index.py

@@ -23,7 +23,6 @@
 import responses
 from botocore import UNSIGNED
 from botocore.client import Config
-from botocore.exceptions import ParamValidationError
 from botocore.stub import Stubber
 from dateutil.tz import tzutc
 from document_queue import EVENT_PREFIX, RetryError
@@ -979,7 +978,7 @@ def test_index_if_package_select_stats_fail(self, append_mock, select_meta_mock,
         )
 
         select_meta_mock.assert_called_once_with(self.s3_client, bucket, manifest_key)
-        select_stats_mock.assert_called_once_with(self.s3_client, bucket, manifest_key)
+        select_stats_mock.assert_called_once_with(bucket, manifest_key)
         append_mock.assert_called_once_with({
             "_index": bucket + PACKAGE_INDEX_SUFFIX,
             "_id": key,
@@ -1023,7 +1022,7 @@ def test_index_if_package(self, append_mock, select_meta_mock, select_stats_mock
         )
 
         select_meta_mock.assert_called_once_with(self.s3_client, bucket, manifest_key)
-        select_stats_mock.assert_called_once_with(self.s3_client, bucket, manifest_key)
+        select_stats_mock.assert_called_once_with(bucket, manifest_key)
         append_mock.assert_called_once_with({
             "_index": bucket + PACKAGE_INDEX_SUFFIX,
             "_id": key,
@@ -1182,51 +1181,6 @@ def test_extension_overrides(self):
             assert self._get_contents('foo.txt', '.txt') == ""
             assert self._get_contents('foo.ipynb', '.ipynb') == ""
 
-    @pytest.mark.xfail(
-        raises=ParamValidationError,
-        reason="boto bug https://github.com/boto/botocore/issues/1621",
-        strict=True,
-    )
-    def test_stub_select_object_content(self):
-        """Demonstrate that mocking S3 select with boto3 is broken"""
-        sha_hash = "50f4d0fc2c22a70893a7f356a4929046ce529b53c1ef87e28378d92b884691a5"
-        manifest_key = f"{MANIFEST_PREFIX_V1}{sha_hash}"
-        # this SHOULD work, but due to botocore bugs it does not
-        self.s3_stubber.add_response(
-            method="select_object_content",
-            service_response={
-                "ResponseMetadata": ANY,
-                # it is sadly not possible to mock S3 select responses because
-                # boto incorrectly believes "Payload"'s value should be a dict
-                # but it's really an iterable in realworld code
-                # see https://github.com/boto/botocore/issues/1621
-                "Payload": [
-                    {
-                        "Stats": {}
-                    },
-                    {
-                        "Records": {
-                            "Payload": json.dumps(MANIFEST_DATA).encode(),
-                        },
-                    },
-                    {
-                        "End": {}
-                    },
-                ]
-            },
-            expected_params={
-                "Bucket": "test-bucket",
-                "Key": manifest_key,
-                "Expression": index.SELECT_PACKAGE_META,
-                "ExpressionType": "SQL",
-                "InputSerialization": {
-                    'JSON': {'Type': 'LINES'},
-                    'CompressionType': 'NONE'
-                },
-                "OutputSerialization": {'JSON': {'RecordDelimiter': '\n'}}
-            }
-        )
-
     def test_synthetic_copy_event(self):
         """check synthetic ObjectCreated:Copy event vs organic obtained on 26-May-2020
         (bucket versioning on)