Source file: do not read whole file on check and discover (#24278)

* #1681 source file: do not read whole file on check and discover

* #1681 source file: upd changelog

* #1681 source file: add allowed hosts

* auto-bump connector version

---------

Co-authored-by: Octavia Squidington III <octavia-squidington-iii@users.noreply.github.com>

airbyte-config/init/src/main/resources/seed/source_definitions.yaml

@@ -601,11 +601,14 @@
 - name: File (CSV, JSON, Excel, Feather, Parquet)
   sourceDefinitionId: 778daa7c-feaf-4db6-96f3-70fd645acc77
   dockerRepository: airbyte/source-file
-  dockerImageTag: 0.2.34
+  dockerImageTag: 0.2.35
   documentationUrl: https://docs.airbyte.com/integrations/sources/file
   icon: file.svg
   sourceType: file
   releaseStage: generally_available
+  allowedHosts:
+    hosts:
+      - "*"
 - name: Firebase Realtime Database
   sourceDefinitionId: acb5f973-a565-441e-992f-4946f3e65662
   dockerRepository: airbyte/source-firebase-realtime-database

airbyte-config/init/src/main/resources/seed/source_specs.yaml

@@ -4358,7 +4358,7 @@
     supportsNormalization: false
     supportsDBT: false
     supported_destination_sync_modes: []
-- dockerImage: "airbyte/source-file:0.2.34"
+- dockerImage: "airbyte/source-file:0.2.35"
   spec:
     documentationUrl: "https://docs.airbyte.com/integrations/sources/file"
     connectionSpecification:

airbyte-integrations/connectors/source-file-secure/Dockerfile

@@ -1,4 +1,4 @@
-FROM airbyte/source-file:0.2.34
+FROM airbyte/source-file:0.2.35
 
 WORKDIR /airbyte/integration_code
 COPY source_file_secure ./source_file_secure
@@ -9,5 +9,5 @@ RUN pip install .
 ENV AIRBYTE_ENTRYPOINT "python /airbyte/integration_code/main.py"
 ENTRYPOINT ["python", "/airbyte/integration_code/main.py"]
 
-LABEL io.airbyte.version=0.2.34
+LABEL io.airbyte.version=0.2.35
 LABEL io.airbyte.name=airbyte/source-file-secure

airbyte-integrations/connectors/source-file/Dockerfile

@@ -17,5 +17,5 @@ COPY source_file ./source_file
 ENV AIRBYTE_ENTRYPOINT "python /airbyte/integration_code/main.py"
 ENTRYPOINT ["python", "/airbyte/integration_code/main.py"]
 
-LABEL io.airbyte.version=0.2.34
+LABEL io.airbyte.version=0.2.35
 LABEL io.airbyte.name=airbyte/source-file

airbyte-integrations/connectors/source-file/integration_tests/client_storage_providers_test.py

@@ -59,7 +59,7 @@ def test__read_file_not_found(provider_config, provider_name, file_path, file_fo
 )
 def test__streams_from_ssh_providers(provider_config, provider_name, file_path, file_format):
     client = Client(dataset_name="output", format=file_format, url=file_path, provider=provider_config(provider_name))
-    streams = list(client.streams)
+    streams = list(client.streams())
     assert len(streams) == 1
     assert streams[0].json_schema["properties"] == {
         "header1": {"type": ["string", "null"]},

airbyte-integrations/connectors/source-file/integration_tests/file_formats_test.py

@@ -4,7 +4,6 @@
 
 
 from pathlib import Path
-from unittest.mock import patch
 
 import pytest
 from airbyte_cdk import AirbyteLogger
@@ -79,29 +78,3 @@ def run_load_nested_json_schema(config, expected_columns=10, expected_rows=42):
     df = data_list[0]
     assert len(df) == expected_rows  # DataFrame should have 42 items
     return df
-
-
-# https://github.com/airbytehq/alpha-beta-issues/issues/174
-# this is to ensure we make all conditions under which the bug is reproduced, i.e.
-# - chunk size < file size
-# - column type in the last chunk is not `string`
-@patch("source_file.client.Client.CSV_CHUNK_SIZE", 1)
-def test_csv_schema():
-    source = SourceFile()
-    file_path = str(SAMPLE_DIRECTORY.parent.joinpath("discover.csv"))
-    config = {"dataset_name": "test", "format": "csv", "url": file_path, "provider": {"storage": "local"}}
-    catalog = source.discover(logger=AirbyteLogger(), config=config).dict()
-    assert len(catalog["streams"]) == 1
-    schema = catalog["streams"][0]["json_schema"]
-    assert schema == {
-        "$schema": "http://json-schema.org/draft-07/schema#",
-        "properties": {
-            "Address": {"type": ["string", "null"]},
-            "City": {"type": ["string", "null"]},
-            "First Name": {"type": ["string", "null"]},
-            "Last Name": {"type": ["string", "null"]},
-            "State": {"type": ["string", "null"]},
-            "zip_code": {"type": ["string", "null"]},
-        },
-        "type": "object",
-    }

airbyte-integrations/connectors/source-file/source_file/client.py

@@ -4,6 +4,7 @@
 
 
 import json
+import sys
 import tempfile
 import traceback
 import urllib
@@ -288,11 +289,12 @@ def load_yaml(self, fp):
         if self._reader_format == "yaml":
             return pd.DataFrame(safe_load(fp))
 
-    def load_dataframes(self, fp, skip_data=False) -> Iterable:
+    def load_dataframes(self, fp, skip_data=False, read_sample_chunk: bool = False) -> Iterable:
         """load and return the appropriate pandas dataframe.
 
         :param fp: file-like object to read from
         :param skip_data: limit reading data
+        :param read_sample_chunk: indicates whether a single chunk should only be read to generate schema
         :return: a list of dataframe loaded from files described in the configuration
         """
         readers = {
@@ -321,11 +323,16 @@ def load_dataframes(self, fp, skip_data=False) -> Iterable:
         reader_options = {**self._reader_options}
         try:
             if self._reader_format == "csv":
+                bytes_read = 0
                 reader_options["chunksize"] = self.CSV_CHUNK_SIZE
                 if skip_data:
                     reader_options["nrows"] = 0
                     reader_options["index_col"] = 0
-                yield from reader(fp, **reader_options)
+                for record in reader(fp, **reader_options):
+                    bytes_read += sys.getsizeof(record)
+                    yield record
+                    if read_sample_chunk and bytes_read >= self.CSV_CHUNK_SIZE:
+                        return
             elif self._reader_options == "excel_binary":
                 reader_options["engine"] = "pyxlsb"
                 yield from reader(fp, **reader_options)
@@ -393,13 +400,17 @@ def _cache_stream(self, fp):
         fp.close()
         return fp_tmp
 
-    def _stream_properties(self, fp):
+    def _stream_properties(self, fp, empty_schema: bool = False, read_sample_chunk: bool = False):
+        """
+        empty_schema param is used to check connectivity, i.e. we only read a header and do not produce stream properties
+        read_sample_chunk is used to determine if just one chunk should be read to generate schema
+        """
         if self._reader_format == "yaml":
             df_list = [self.load_yaml(fp)]
         else:
             if self.binary_source:
                 fp = self._cache_stream(fp)
-            df_list = self.load_dataframes(fp, skip_data=False)
+            df_list = self.load_dataframes(fp, skip_data=empty_schema, read_sample_chunk=read_sample_chunk)
         fields = {}
         for df in df_list:
             for col in df.columns:
@@ -408,8 +419,7 @@ def _stream_properties(self, fp):
                 fields[col] = self.dtype_to_json_type(prev_frame_column_type, df[col].dtype)
         return {field: {"type": [fields[field], "null"]} for field in fields}
 
-    @property
-    def streams(self) -> Iterable:
+    def streams(self, empty_schema: bool = False) -> Iterable:
         """Discovers available streams"""
         # TODO handle discovery of directories of multiple files instead
         with self.reader.open() as fp:
@@ -419,6 +429,6 @@ def streams(self) -> Iterable:
                 json_schema = {
                     "$schema": "http://json-schema.org/draft-07/schema#",
                     "type": "object",
-                    "properties": self._stream_properties(fp),
+                    "properties": self._stream_properties(fp, empty_schema=empty_schema, read_sample_chunk=True),
                 }
         yield AirbyteStream(name=self.stream_name, json_schema=json_schema, supported_sync_modes=[SyncMode.full_refresh])

airbyte-integrations/connectors/source-file/source_file/source.py

@@ -79,7 +79,8 @@ def _get_client(self, config: Mapping):
 
         return client
 
-    def _validate_and_transform(self, config: Mapping[str, Any]):
+    @staticmethod
+    def _validate_and_transform(config: Mapping[str, Any]):
         if "reader_options" in config:
             try:
                 config["reader_options"] = json.loads(config["reader_options"])
@@ -108,9 +109,8 @@ def check(self, logger, config: Mapping) -> AirbyteConnectionStatus:
         client = self._get_client(config)
         source_url = client.reader.full_url
         try:
-            with client.reader.open():
-                list(client.streams)
-                return AirbyteConnectionStatus(status=Status.SUCCEEDED)
+            list(client.streams(empty_schema=True))
+            return AirbyteConnectionStatus(status=Status.SUCCEEDED)
         except (TypeError, ValueError, ConfigurationError) as err:
             reason = f"Failed to load {source_url}\n Please check File Format and Reader Options are set correctly. \n{repr(err)}"
             logger.error(reason)
@@ -127,13 +127,13 @@ def discover(self, logger: AirbyteLogger, config: Mapping) -> AirbyteCatalog:
         """
         config = self._validate_and_transform(config)
         client = self._get_client(config)
-        name = client.stream_name
+        name, full_url = client.stream_name, client.reader.full_url
 
-        logger.info(f"Discovering schema of {name} at {client.reader.full_url}...")
+        logger.info(f"Discovering schema of {name} at {full_url}...")
         try:
-            streams = list(client.streams)
+            streams = list(client.streams())
         except Exception as err:
-            reason = f"Failed to discover schemas of {name} at {client.reader.full_url}: {repr(err)}\n{traceback.format_exc()}"
+            reason = f"Failed to discover schemas of {name} at {full_url}: {repr(err)}\n{traceback.format_exc()}"
             logger.error(reason)
             raise err
         return AirbyteCatalog(streams=streams)

connectors.md

@@ -71,7 +71,7 @@
 | **Facebook Pages** | <img alt="Facebook Pages icon" src="https://raw.githubusercontent.com/airbytehq/airbyte/master/airbyte-config/init/src/main/resources/icons/facebook.svg" height="30" height="30"/> | Source | airbyte/source-facebook-pages:0.2.3 | beta | [link](https://docs.airbyte.com/integrations/sources/facebook-pages) | [code](https://github.com/airbytehq/airbyte/tree/master/airbyte-integrations/connectors/source-facebook-pages) | <small>`010eb12f-837b-4685-892d-0a39f76a98f5`</small> |
 | **Fastbill** | <img alt="Fastbill icon" src="https://raw.githubusercontent.com/airbytehq/airbyte/master/airbyte-config/init/src/main/resources/icons/fastbill.svg" height="30" height="30"/> | Source | airbyte/source-fastbill:0.1.0 | alpha | [link](https://docs.airbyte.com/integrations/sources/fastbill) | [code](https://github.com/airbytehq/airbyte/tree/master/airbyte-integrations/connectors/source-fastbill) | <small>`eb3e9c1c-0467-4eb7-a172-5265e04ccd0a`</small> |
 | **Fauna** | <img alt="Fauna icon" src="https://raw.githubusercontent.com/airbytehq/airbyte/master/airbyte-config/init/src/main/resources/icons/fauna.svg" height="30" height="30"/> | Source | airbyte/source-fauna:0.1.1 | alpha | [link](https://docs.airbyte.com/integrations/sources/fauna) | [code](https://github.com/airbytehq/airbyte/tree/master/airbyte-integrations/connectors/source-fauna) | <small>`3825db3e-c94b-42ac-bd53-b5a9507ace2b`</small> |
-| **File (CSV, JSON, Excel, Feather, Parquet)** | <img alt="File (CSV, JSON, Excel, Feather, Parquet) icon" src="https://raw.githubusercontent.com/airbytehq/airbyte/master/airbyte-config/init/src/main/resources/icons/file.svg" height="30" height="30"/> | Source | airbyte/source-file:0.2.34 | generally_available | [link](https://docs.airbyte.com/integrations/sources/file) | [code](https://github.com/airbytehq/airbyte/tree/master/airbyte-integrations/connectors/source-file) | <small>`778daa7c-feaf-4db6-96f3-70fd645acc77`</small> |
+| **File (CSV, JSON, Excel, Feather, Parquet)** | <img alt="File (CSV, JSON, Excel, Feather, Parquet) icon" src="https://raw.githubusercontent.com/airbytehq/airbyte/master/airbyte-config/init/src/main/resources/icons/file.svg" height="30" height="30"/> | Source | airbyte/source-file:0.2.35 | generally_available | [link](https://docs.airbyte.com/integrations/sources/file) | [code](https://github.com/airbytehq/airbyte/tree/master/airbyte-integrations/connectors/source-file) | <small>`778daa7c-feaf-4db6-96f3-70fd645acc77`</small> |
 | **Firebase Realtime Database** | x | Source | airbyte/source-firebase-realtime-database:0.1.0 | alpha | [link](https://docs.airbyte.io/integrations/sources/firebase-realtime-database) | [code](https://github.com/airbytehq/airbyte/tree/master/airbyte-integrations/connectors/source-firebase-realtime-database) | <small>`acb5f973-a565-441e-992f-4946f3e65662`</small> |
 | **Firebolt** | <img alt="Firebolt icon" src="https://raw.githubusercontent.com/airbytehq/airbyte/master/airbyte-config/init/src/main/resources/icons/firebolt.svg" height="30" height="30"/> | Source | airbyte/source-firebolt:0.2.0 | alpha | [link](https://docs.airbyte.com/integrations/sources/firebolt) | [code](https://github.com/airbytehq/airbyte/tree/master/airbyte-integrations/connectors/source-firebolt) | <small>`6f2ac653-8623-43c4-8950-19218c7caf3d`</small> |
 | **Flexport** | x | Source | airbyte/source-flexport:0.1.0 | alpha | [link](https://docs.airbyte.com/integrations/sources/flexport) | [code](https://github.com/airbytehq/airbyte/tree/master/airbyte-integrations/connectors/source-flexport) | <small>`f95337f1-2ad1-4baf-922f-2ca9152de630`</small> |