File-based CDK + Source S3 (v4): Pass configured file encoding to str…

…eam reader (airbytehq#29110)

* Add encoding to open_file interface

* pass the encoding set in the config

* cleanup

* cleanup

* Automated Commit - Formatting Changes

* Add missing test

* Automated Commit - Formatting Changes

* Update infer_schema too

* Automated Commit - Formatting Changes

* Update unit test

* add a unit test

* fix

* format

* format

* remove newline

* use a mock

* fix

* format

---------

Co-authored-by: girarda <girarda@users.noreply.github.com>

airbyte-cdk/python/airbyte_cdk/sources/file_based/config/csv_format.py

@@ -98,7 +98,7 @@ def validate_quote_char(cls, v: str) -> str:
 
     @validator("escape_char")
     def validate_escape_char(cls, v: str) -> str:
-        if len(v) != 1:
+        if v is not None and len(v) != 1:
             raise ValueError("escape_char should only be one character")
         return v
 

airbyte-cdk/python/airbyte_cdk/sources/file_based/file_based_stream_reader.py

@@ -44,7 +44,7 @@ def config(self, value: AbstractFileBasedSpec) -> None:
         ...
 
     @abstractmethod
-    def open_file(self, file: RemoteFile, mode: FileReadMode, logger: logging.Logger) -> IOBase:
+    def open_file(self, file: RemoteFile, mode: FileReadMode, encoding: Optional[str], logger: logging.Logger) -> IOBase:
         """
         Return a file handle for reading.
 

airbyte-cdk/python/airbyte_cdk/sources/file_based/file_types/avro_parser.py

@@ -39,6 +39,8 @@
 
 
 class AvroParser(FileTypeParser):
+    ENCODING = None
+
     async def infer_schema(
         self,
         config: FileBasedStreamConfig,
@@ -50,7 +52,7 @@ async def infer_schema(
         if not isinstance(avro_format, AvroFormat):
             raise ValueError(f"Expected ParquetFormat, got {avro_format}")
 
-        with stream_reader.open_file(file, self.file_read_mode, logger) as fp:
+        with stream_reader.open_file(file, self.file_read_mode, self.ENCODING, logger) as fp:
             avro_reader = fastavro.reader(fp)
             avro_schema = avro_reader.writer_schema
         if not avro_schema["type"] == "record":
@@ -135,7 +137,7 @@ def parse_records(
         if not isinstance(avro_format, AvroFormat):
             raise ValueError(f"Expected ParquetFormat, got {avro_format}")
 
-        with stream_reader.open_file(file, self.file_read_mode, logger) as fp:
+        with stream_reader.open_file(file, self.file_read_mode, self.ENCODING, logger) as fp:
             avro_reader = fastavro.reader(fp)
             schema = avro_reader.writer_schema
             schema_field_name_to_type = {field["name"]: field["type"] for field in schema["fields"]}

airbyte-cdk/python/airbyte_cdk/sources/file_based/file_types/csv_parser.py

@@ -47,7 +47,7 @@ async def infer_schema(
             doublequote=config_format.double_quote,
             quoting=config_to_quoting.get(config_format.quoting_behavior, csv.QUOTE_MINIMAL),
         )
-        with stream_reader.open_file(file, self.file_read_mode, logger) as fp:
+        with stream_reader.open_file(file, self.file_read_mode, config_format.encoding, logger) as fp:
             # todo: the existing InMemoryFilesSource.open_file() test source doesn't currently require an encoding, but actual
             #  sources will likely require one. Rather than modify the interface now we can wait until the real use case
             headers = self._get_headers(fp, config_format, dialect_name)
@@ -78,7 +78,7 @@ def parse_records(
             doublequote=config_format.double_quote,
             quoting=config_to_quoting.get(config_format.quoting_behavior, csv.QUOTE_MINIMAL),
         )
-        with stream_reader.open_file(file, self.file_read_mode, logger) as fp:
+        with stream_reader.open_file(file, self.file_read_mode, config_format.encoding, logger) as fp:
             # todo: the existing InMemoryFilesSource.open_file() test source doesn't currently require an encoding, but actual
             #  sources will likely require one. Rather than modify the interface now we can wait until the real use case
             self._skip_rows_before_header(fp, config_format.skip_rows_before_header)

airbyte-cdk/python/airbyte_cdk/sources/file_based/file_types/jsonl_parser.py

@@ -16,6 +16,7 @@
 class JsonlParser(FileTypeParser):
 
     MAX_BYTES_PER_FILE_FOR_SCHEMA_INFERENCE = 1_000_000
+    ENCODING = "utf8"
 
     async def infer_schema(
         self,
@@ -31,7 +32,7 @@ async def infer_schema(
         inferred_schema: Dict[str, Any] = {}
         read_bytes = 0
 
-        with stream_reader.open_file(file, self.file_read_mode, logger) as fp:
+        with stream_reader.open_file(file, self.file_read_mode, self.ENCODING, logger) as fp:
             for line in fp:
                 if read_bytes < self.MAX_BYTES_PER_FILE_FOR_SCHEMA_INFERENCE:
                     line_schema = self.infer_schema_for_record(json.loads(line))
@@ -53,7 +54,7 @@ def parse_records(
         stream_reader: AbstractFileBasedStreamReader,
         logger: logging.Logger,
     ) -> Iterable[Dict[str, Any]]:
-        with stream_reader.open_file(file, self.file_read_mode, logger) as fp:
+        with stream_reader.open_file(file, self.file_read_mode, self.ENCODING, logger) as fp:
             for line in fp:
                 yield json.loads(line)
 

airbyte-cdk/python/airbyte_cdk/sources/file_based/file_types/parquet_parser.py

@@ -11,13 +11,17 @@
 import pyarrow as pa
 import pyarrow.parquet as pq
 from airbyte_cdk.sources.file_based.config.file_based_stream_config import FileBasedStreamConfig, ParquetFormat
+from airbyte_cdk.sources.file_based.exceptions import ConfigValidationError, FileBasedSourceError
 from airbyte_cdk.sources.file_based.file_based_stream_reader import AbstractFileBasedStreamReader, FileReadMode
 from airbyte_cdk.sources.file_based.file_types.file_type_parser import FileTypeParser
 from airbyte_cdk.sources.file_based.remote_file import RemoteFile
 from pyarrow import Scalar
 
 
 class ParquetParser(FileTypeParser):
+
+    ENCODING = None
+
     async def infer_schema(
         self,
         config: FileBasedStreamConfig,
@@ -29,7 +33,7 @@ async def infer_schema(
         if not isinstance(parquet_format, ParquetFormat):
             raise ValueError(f"Expected ParquetFormat, got {parquet_format}")
 
-        with stream_reader.open_file(file, self.file_read_mode, logger) as fp:
+        with stream_reader.open_file(file, self.file_read_mode, self.ENCODING, logger) as fp:
             parquet_file = pq.ParquetFile(fp)
             parquet_schema = parquet_file.schema_arrow
 
@@ -50,8 +54,9 @@ def parse_records(
     ) -> Iterable[Dict[str, Any]]:
         parquet_format = config.format or ParquetFormat()
         if not isinstance(parquet_format, ParquetFormat):
-            raise ValueError(f"Expected ParquetFormat, got {parquet_format}")  # FIXME test this branch!
-        with stream_reader.open_file(file, self.file_read_mode, logger) as fp:
+            logger.info(f"Expected ParquetFormat, got {parquet_format}")
+            raise ConfigValidationError(FileBasedSourceError.CONFIG_VALIDATION_ERROR)
+        with stream_reader.open_file(file, self.file_read_mode, self.ENCODING, logger) as fp:
             reader = pq.ParquetFile(fp)
             partition_columns = {x.split("=")[0]: x.split("=")[1] for x in self._extract_partitions(file.uri)}
             for row_group in range(reader.num_row_groups):

airbyte-cdk/python/unit_tests/sources/file_based/file_types/test_csv_parser.py

@@ -2,13 +2,20 @@
 # Copyright (c) 2023 Airbyte, Inc., all rights reserved.
 #
 
+import asyncio
+import io
 import logging
+from datetime import datetime
+from unittest import mock
 from unittest.mock import MagicMock, Mock
 
 import pytest
 from airbyte_cdk.sources.file_based.config.csv_format import DEFAULT_FALSE_VALUES, DEFAULT_TRUE_VALUES, CsvFormat
+from airbyte_cdk.sources.file_based.config.file_based_stream_config import FileBasedStreamConfig
 from airbyte_cdk.sources.file_based.exceptions import RecordParseError
+from airbyte_cdk.sources.file_based.file_based_stream_reader import FileReadMode
 from airbyte_cdk.sources.file_based.file_types.csv_parser import CsvParser, _cast_types
+from airbyte_cdk.sources.file_based.remote_file import RemoteFile
 
 PROPERTY_TYPES = {
     "col1": "null",
@@ -96,3 +103,38 @@ def test_read_and_cast_types(reader_values, expected_rows):
             list(parser._read_and_cast_types(reader, schema, config_format, logger))
     else:
         assert expected_rows == list(parser._read_and_cast_types(reader, schema, config_format, logger))
+
+
+def test_encoding_is_passed_to_stream_reader():
+    parser = CsvParser()
+    encoding = "ascii"
+    stream_reader = Mock()
+    mock_obj = stream_reader.open_file.return_value
+    mock_obj.__enter__ = Mock(return_value=io.StringIO("c1,c2\nv1,v2"))
+    mock_obj.__exit__ = Mock(return_value=None)
+    file = RemoteFile(uri="s3://bucket/key.csv", last_modified=datetime.now())
+    config = FileBasedStreamConfig(
+        name="test",
+        validation_policy="Emit Record",
+        file_type="csv",
+        format=CsvFormat(encoding=encoding)
+    )
+    list(parser.parse_records(config, file, stream_reader, logger))
+    stream_reader.open_file.assert_has_calls([
+        mock.call(file, FileReadMode.READ, encoding, logger),
+        mock.call().__enter__(),
+        mock.call().__exit__(None, None, None),
+    ])
+
+    mock_obj.__enter__ = Mock(return_value=io.StringIO("c1,c2\nv1,v2"))
+    loop = asyncio.get_event_loop()
+    loop.run_until_complete(parser.infer_schema(config, file, stream_reader, logger))
+    stream_reader.open_file.assert_called_with(file, FileReadMode.READ, encoding, logger)
+    stream_reader.open_file.assert_has_calls([
+        mock.call(file, FileReadMode.READ, encoding, logger),
+        mock.call().__enter__(),
+        mock.call().__exit__(None, None, None),
+        mock.call(file, FileReadMode.READ, encoding, logger),
+        mock.call().__enter__(),
+        mock.call().__exit__(None, None, None),
+    ])

airbyte-cdk/python/unit_tests/sources/file_based/helpers.py

@@ -43,7 +43,7 @@ def get_matching_files(
 
 
 class TestErrorOpenFileInMemoryFilesStreamReader(InMemoryFilesStreamReader):
-    def open_file(self, file: RemoteFile, file_read_mode: FileReadMode, logger: logging.Logger) -> IOBase:
+    def open_file(self, file: RemoteFile, file_read_mode: FileReadMode, encoding: Optional[str], logger: logging.Logger) -> IOBase:
         raise Exception("Error opening file")
 
 

airbyte-cdk/python/unit_tests/sources/file_based/in_memory_files_source.py

@@ -92,7 +92,7 @@ def get_matching_files(
             for f, data in self.files.items()
         ], globs)
 
-    def open_file(self, file: RemoteFile, mode: FileReadMode, logger: logging.Logger) -> IOBase:
+    def open_file(self, file: RemoteFile, mode: FileReadMode, encoding: Optional[str], logger: logging.Logger) -> IOBase:
         if self.file_type == "csv":
             return self._make_csv_file_contents(file.uri)
         elif self.file_type == "jsonl":
@@ -144,7 +144,7 @@ class TemporaryParquetFilesStreamReader(InMemoryFilesStreamReader):
     A file reader that writes RemoteFiles to a temporary file and then reads them back.
     """
 
-    def open_file(self, file: RemoteFile, mode: FileReadMode, logger: logging.Logger) -> IOBase:
+    def open_file(self, file: RemoteFile, mode: FileReadMode, encoding: Optional[str], logger: logging.Logger) -> IOBase:
         return io.BytesIO(self._create_file(file.uri))
 
     def _create_file(self, file_name: str) -> bytes:
@@ -165,7 +165,7 @@ class TemporaryAvroFilesStreamReader(InMemoryFilesStreamReader):
     A file reader that writes RemoteFiles to a temporary file and then reads them back.
     """
 
-    def open_file(self, file: RemoteFile, mode: FileReadMode, logger: logging.Logger) -> IOBase:
+    def open_file(self, file: RemoteFile, mode: FileReadMode, encoding: Optional[str], logger: logging.Logger) -> IOBase:
         return io.BytesIO(self._make_file_contents(file.uri))
 
     def _make_file_contents(self, file_name: str) -> bytes:

airbyte-cdk/python/unit_tests/sources/file_based/scenarios/parquet_scenarios.py

@@ -6,6 +6,7 @@
 import decimal
 
 import pyarrow as pa
+from airbyte_cdk.sources.file_based.exceptions import SchemaInferenceError
 from unit_tests.sources.file_based.in_memory_files_source import TemporaryParquetFilesStreamReader
 from unit_tests.sources.file_based.scenarios.scenario_builder import TestScenarioBuilder
 
@@ -644,3 +645,119 @@
         }
     )
 ).build()
+
+parquet_file_with_decimal_legacy_config_scenario = (
+    TestScenarioBuilder()
+    .set_name("parquet_file_with_decimal_legacy_config")
+    .set_config(
+        {
+            "streams": [
+                {
+                    "name": "stream1",
+                    "file_type": "parquet",
+                    "format": {
+                        "filetype": "parquet",
+                    },
+                    "globs": ["*"],
+                    "validation_policy": "emit_record",
+                }
+            ]
+        }
+    )
+    .set_stream_reader(TemporaryParquetFilesStreamReader(files=_parquet_file_with_decimal, file_type="parquet"))
+    .set_file_type("parquet")
+    .set_expected_records(
+        [
+            {"data": {"col1": 13.00, "_ab_source_file_last_modified": "2023-06-05T03:54:07.000000Z",
+                      "_ab_source_file_url": "a.parquet"}, "stream": "stream1"},
+        ]
+    )
+    .set_expected_catalog(
+        {
+            "streams": [
+                {
+                    "default_cursor_field": ["_ab_source_file_last_modified"],
+                    "json_schema": {
+                        "type": "object",
+                        "properties": {
+                            "col1": {
+                                "type": ["null", "number"]
+                            },
+                            "_ab_source_file_last_modified": {
+                                "type": "string"
+                            },
+                            "_ab_source_file_url": {
+                                "type": "string"
+                            },
+                        }
+                    },
+                    "name": "stream1",
+                    "source_defined_cursor": True,
+                    "supported_sync_modes": ["full_refresh", "incremental"],
+                }
+            ]
+        }
+    )
+).build()
+
+parquet_with_invalid_config_scenario = (
+    TestScenarioBuilder()
+    .set_name("parquet_with_invalid_config")
+    .set_config(
+        {
+            "streams": [
+                {
+                    "name": "stream1",
+                    "file_type": "parquet",
+                    "globs": ["*"],
+                    "validation_policy": "Emit Record",
+                    "format": {
+                        "filetype": "csv"
+                    }
+                }
+            ]
+        }
+    )
+    .set_stream_reader(TemporaryParquetFilesStreamReader(files=_single_parquet_file, file_type="parquet"))
+    .set_file_type("parquet")
+    .set_expected_records(
+        [
+        ]
+    )
+    .set_expected_logs({"read": [
+        {
+            "level": "ERROR",
+            "message": "Error parsing record"
+        }
+    ]})
+    .set_expected_discover_error(SchemaInferenceError, "Error inferring schema from files")
+    .set_expected_catalog(
+        {
+            "streams": [
+                {
+                    "default_cursor_field": ["_ab_source_file_last_modified"],
+                    "json_schema": {
+                        "type": "object",
+                        "properties": {
+                            "col1": {
+                                "type": ["null", "string"]
+                            },
+                            "col2": {
+                                "type": ["null", "string"]
+                            },
+                            "_ab_source_file_last_modified": {
+                                "type": "string"
+                            },
+                            "_ab_source_file_url": {
+                                "type": "string"
+                            },
+                        }
+                    },
+                    "name": "stream1",
+                    "source_defined_cursor": True,
+                    "supported_sync_modes": ["full_refresh", "incremental"],
+                }
+            ]
+        }
+    )
+).build()

airbyte-cdk/python/unit_tests/sources/file_based/test_scenarios.py

@@ -98,6 +98,7 @@
     parquet_file_with_decimal_as_string_scenario,
     parquet_file_with_decimal_no_config_scenario,
     parquet_various_types_scenario,
+    parquet_with_invalid_config_scenario,
     single_parquet_scenario,
     single_partitioned_parquet_scenario,
 )
@@ -194,7 +195,8 @@
     avro_file_with_double_as_number_scenario,
     csv_newline_in_values_not_quoted_scenario,
     csv_autogenerate_column_names_scenario,
-    single_partitioned_parquet_scenario
+    parquet_with_invalid_config_scenario,
+    single_partitioned_parquet_scenario,
 ]
 
 

airbyte-integrations/connectors/source-s3/source_s3/v4/stream_reader.py

@@ -89,15 +89,15 @@ def get_matching_files(self, globs: List[str], logger: logging.Logger) -> Iterab
             ) from exc
 
     @contextmanager
-    def open_file(self, file: RemoteFile, mode: FileReadMode, logger: logging.Logger) -> IOBase:
+    def open_file(self, file: RemoteFile, mode: FileReadMode, encoding: Optional[str], logger: logging.Logger) -> IOBase:
         try:
             params = {"client": self.s3_client}
         except Exception as exc:
             raise exc
 
         logger.debug(f"try to open {file.uri}")
         try:
-            result = smart_open.open(f"s3://{self.config.bucket}/{file.uri}", transport_params=params, mode=mode.value)
+            result = smart_open.open(f"s3://{self.config.bucket}/{file.uri}", transport_params=params, mode=mode.value, encoding=encoding)
         except OSError:
             logger.warning(
                 f"We don't have access to {file.uri}. The file appears to have become unreachable during sync."