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b/sources/filesystem/README.md @@ -1,18 +1,18 @@ # Readers Source & Filesystem -This verified source easily streams files from AWS S3, GCS, Azure, or local filesystem using the -reader source. +This verified source easily streams files from AWS S3, GCS, Azure, or local filesystem using the reader source. Sources and resources that can be used with this verified source are: -| Name | Type | Description | -|--------------|----------------------|---------------------------------------------------------------------------| -| readers | Source | Lists and reads files with resource `filesystem` and readers transformers | -| filesystem | Resource | Lists files in `bucket_url` using `file_glob` pattern | -| read_csv | Resource-transformer | Reads CSV file with "Pandas" chunk by chunk | -| read_jsonl | Resource-transformer | Reads JSONL file content and extracts the data | -| read_parquet | Resource-transformer | Reads Parquet file content and extracts the data with "Pyarrow" | +| Name | Type | Description | +|-----------------|----------------------|---------------------------------------------------------------------------| +| readers | Source | Lists and reads files with resource `filesystem` and readers transformers | +| filesystem | Resource | Lists files in `bucket_url` using `file_glob` pattern | +| read_csv | Resource-transformer | Reads CSV file with "Pandas" chunk by chunk | +| read_csv_duckdb | Resource-transformer | Reads CSV file with DuckDB engine chunk by chunk | +| read_jsonl | Resource-transformer | Reads JSONL file content and extracts the data | +| read_parquet | Resource-transformer | Reads Parquet file content and extracts the data with "Pyarrow" | ## Initialize the source diff --git a/sources/filesystem/__init__.py b/sources/filesystem/__init__.py index e0d8d3b24..c6452543e 100644 --- a/sources/filesystem/__init__.py +++ b/sources/filesystem/__init__.py @@ -10,9 +10,14 @@ from .helpers import ( AbstractFileSystem, FilesystemConfigurationResource, - fsspec_from_resource, ) -from .readers import ReadersSource, _read_csv, _read_jsonl, _read_parquet +from .readers import ( + ReadersSource, + _read_csv, + _read_csv_duckdb, + _read_jsonl, + _read_parquet, +) from .settings import DEFAULT_CHUNK_SIZE @@ -39,6 +44,8 @@ def readers( | dlt.transformer(name="read_jsonl")(_read_jsonl), filesystem(bucket_url, credentials, file_glob=file_glob) | dlt.transformer(name="read_parquet")(_read_parquet), + filesystem(bucket_url, credentials, file_glob=file_glob) + | dlt.transformer(name="read_csv_duckdb")(_read_csv_duckdb), ) @@ -89,3 +96,4 @@ def filesystem( read_csv = dlt.transformer(standalone=True)(_read_csv) read_jsonl = dlt.transformer(standalone=True)(_read_jsonl) read_parquet = dlt.transformer(standalone=True)(_read_parquet) +read_csv_duckdb = dlt.transformer(standalone=True)(_read_csv_duckdb) diff --git a/sources/filesystem/helpers.py b/sources/filesystem/helpers.py index 225b171b7..8bd11705d 100644 --- a/sources/filesystem/helpers.py +++ b/sources/filesystem/helpers.py @@ -1,10 +1,11 @@ """Helpers for the filesystem resource.""" -from typing import Optional, Type, Union, TYPE_CHECKING, Any +from typing import TYPE_CHECKING, Any, Dict, Iterable, List, Optional, Type, Union from fsspec import AbstractFileSystem # type: ignore from dlt.common.configuration import resolve_type +from dlt.common.typing import TDataItem -from dlt.sources import DltResource, DltSource +from dlt.sources import DltResource from dlt.sources.filesystem import fsspec_filesystem from dlt.sources.config import configspec, with_config from dlt.sources.credentials import ( @@ -46,3 +47,52 @@ def _get_fsspec( filesystem_instance.explicit_args.get("bucket_url", None), filesystem_instance.explicit_args.get("credentials", None), ) + + +def add_columns(columns: List[str], rows: List[List[Any]]) -> List[Dict[str, Any]]: + """Adds column names to the given rows. + + Args: + columns (List[str]): The column names. + rows (List[List[Any]]): The rows. + + Returns: + List[Dict[str, Any]]: The rows with column names. + """ + result = [] + for row in rows: + result.append(dict(zip(columns, row))) + + return result + + +def fetch_arrow(file_data, chunk_size: int) -> Iterable[TDataItem]: # type: ignore + """Fetches data from the given CSV file. + + Args: + file_data (DuckDBPyRelation): The CSV file data. + chunk_size (int): The number of rows to read at once. + + Yields: + Iterable[TDataItem]: Data items, read from the given CSV file. + """ + batcher = file_data.fetch_arrow_reader(batch_size=chunk_size) + yield from batcher + + +def fetch_json(file_data, chunk_size: int) -> List[Dict[str, Any]]: # type: ignore + """Fetches data from the given CSV file. + + Args: + file_data (DuckDBPyRelation): The CSV file data. + chunk_size (int): The number of rows to read at once. + + Yields: + Iterable[TDataItem]: Data items, read from the given CSV file. + """ + while True: + batch = file_data.fetchmany(chunk_size) + if not batch: + break + + yield add_columns(file_data.columns, batch) diff --git a/sources/filesystem/readers.py b/sources/filesystem/readers.py index c59037d71..bd5f3575c 100644 --- a/sources/filesystem/readers.py +++ b/sources/filesystem/readers.py @@ -1,10 +1,12 @@ -from typing import TYPE_CHECKING, Any, Iterator +from typing import TYPE_CHECKING, Any, Dict, Iterator, Optional from dlt.common import json from dlt.common.typing import copy_sig from dlt.sources import TDataItems, DltResource, DltSource from dlt.sources.filesystem import FileItemDict +from .helpers import fetch_arrow, fetch_json + def _read_csv( items: Iterator[FileItemDict], chunksize: int = 10000, **pandas_kwargs: Any @@ -74,6 +76,40 @@ def _read_parquet( yield rows.to_pylist() +def _read_csv_duckdb( + items: Iterator[FileItemDict], + chunk_size: Optional[int] = 5000, + use_pyarrow: bool = False, + **duckdb_kwargs: Any +) -> Iterator[TDataItems]: + """A resource to extract data from the given CSV files. + + Uses DuckDB engine to import and cast CSV data. + + Args: + items (Iterator[FileItemDict]): CSV files to read. + chunk_size (Optional[int]): + The number of rows to read at once. Defaults to 5000. + use_pyarrow (bool): + Whether to use `pyarrow` to read the data and designate + data schema. If set to False (by default), JSON is used. + duckdb_kwargs (Dict): + Additional keyword arguments to pass to the `read_csv()`. + + Returns: + Iterable[TDataItem]: Data items, read from the given CSV files. + """ + import duckdb + + helper = fetch_arrow if use_pyarrow else fetch_json + + for item in items: + with item.open() as f: + file_data = duckdb.from_csv_auto(f, **duckdb_kwargs) # type: ignore + + yield from helper(file_data, chunk_size) + + if TYPE_CHECKING: class ReadersSource(DltSource): @@ -91,5 +127,9 @@ def read_jsonl(self) -> DltResource: def read_parquet(self) -> DltResource: ... + @copy_sig(_read_csv_duckdb) + def read_csv_duckdb(self) -> DltResource: + ... + else: ReadersSource = DltSource diff --git a/sources/filesystem_pipeline.py b/sources/filesystem_pipeline.py index af0923851..69094ea65 100644 --- a/sources/filesystem_pipeline.py +++ b/sources/filesystem_pipeline.py @@ -1,21 +1,18 @@ -import json import os import posixpath from typing import Iterator import dlt -from dlt.sources import TDataItem, TDataItems +from dlt.sources import TDataItems try: - from .filesystem import FileItemDict, filesystem, readers, read_csv, read_jsonl, read_parquet # type: ignore + from .filesystem import FileItemDict, filesystem, readers, read_csv # type: ignore except ImportError: from filesystem import ( FileItemDict, filesystem, readers, read_csv, - read_jsonl, - read_parquet, ) @@ -54,6 +51,42 @@ def stream_and_merge_csv() -> None: print(pipeline.last_trace.last_normalize_info) +def read_csv_with_duckdb() -> None: + pipeline = dlt.pipeline( + pipeline_name="standard_filesystem", + destination="duckdb", + dataset_name="met_data_duckdb", + ) + + # load all the CSV data, excluding headers + met_files = readers( + bucket_url=TESTS_BUCKET_URL, file_glob="met_csv/A801/*.csv" + ).read_csv_duckdb(chunk_size=1000, header=True) + + load_info = pipeline.run(met_files) + + print(load_info) + print(pipeline.last_trace.last_normalize_info) + + +def read_csv_duckdb_compressed() -> None: + pipeline = dlt.pipeline( + pipeline_name="standard_filesystem", + destination="duckdb", + dataset_name="taxi_data", + full_refresh=True, + ) + + met_files = readers( + bucket_url=TESTS_BUCKET_URL, + file_glob="gzip/*", + ).read_csv_duckdb() + + load_info = pipeline.run(met_files) + print(load_info) + print(pipeline.last_trace.last_normalize_info) + + def read_parquet_and_jsonl_chunked() -> None: pipeline = dlt.pipeline( pipeline_name="standard_filesystem", @@ -177,3 +210,5 @@ def read_files_incrementally_mtime() -> None: read_parquet_and_jsonl_chunked() read_custom_file_type_excel() read_files_incrementally_mtime() + read_csv_with_duckdb() + read_csv_duckdb_compressed() diff --git a/tests/filesystem/samples/csv/freshman_lbs.csv b/tests/filesystem/samples/csv/freshman_lbs.csv index 31f4bd738..d5992daff 100644 --- a/tests/filesystem/samples/csv/freshman_lbs.csv +++ b/tests/filesystem/samples/csv/freshman_lbs.csv @@ -1,4 +1,4 @@ -Sex,Weight(lbs,Sep),Weight(lbs,Apr),BMI(Sep),BMI(Apr) +"Sex","Weight(lbs,Sep)","Weight(lbs,Apr)","BMI(Sep)","BMI(Apr)" M,159,130,22.02,18.14 M,214,190,19.70,17.44 M,163,152,24.09,22.43 diff --git a/tests/filesystem/samples/gzip/taxi.csv.gz b/tests/filesystem/samples/gzip/taxi.csv.gz new file mode 100644 index 000000000..c74f9c86e Binary files /dev/null and b/tests/filesystem/samples/gzip/taxi.csv.gz differ diff --git a/tests/filesystem/settings.py b/tests/filesystem/settings.py index 5211b4845..a442052b3 100644 --- a/tests/filesystem/settings.py +++ b/tests/filesystem/settings.py @@ -19,6 +19,7 @@ "csv/freshman_lbs.csv", "csv/mlb_players.csv", "csv/mlb_teams_2012.csv", + "gzip/taxi.csv.gz", "jsonl/mlb_players.jsonl", "parquet/mlb_players.parquet", ], diff --git a/tests/filesystem/test_filesystem.py b/tests/filesystem/test_filesystem.py index 3d2936be6..550f4c29d 100644 --- a/tests/filesystem/test_filesystem.py +++ b/tests/filesystem/test_filesystem.py @@ -8,10 +8,10 @@ from sources.filesystem import ( filesystem, readers, - fsspec_from_resource, FileItem, FileItemDict, ) +from sources.filesystem.helpers import fsspec_from_resource from tests.utils import ( assert_load_info, load_table_counts, @@ -144,9 +144,11 @@ def test_standard_readers(bucket_url: str) -> None: # extract pipes with standard readers jsonl_reader = readers(bucket_url, file_glob="**/*.jsonl").read_jsonl() parquet_reader = readers(bucket_url, file_glob="**/*.parquet").read_parquet() - csv_reader = readers(bucket_url, file_glob="**/*.csv").read_csv( + # also read zipped csvs + csv_reader = readers(bucket_url, file_glob="**/*.csv*").read_csv( float_precision="high" ) + csv_duckdb_reader = readers(bucket_url, file_glob="**/*.csv*").read_csv_duckdb() # a step that copies files into test storage def _copy(item: FileItemDict): @@ -174,16 +176,25 @@ def _copy(item: FileItemDict): parquet_reader.with_name("parquet_example"), downloader.with_name("listing"), csv_reader.with_name("csv_example"), + csv_duckdb_reader.with_name("csv_duckdb_example"), ] ) + # pandas incorrectly guesses that taxi dataset has headers so it skips one row + # so we have 1 less row in csv_example than in csv_duckdb_example assert_load_info(load_info) assert load_table_counts( - pipeline, "jsonl_example", "parquet_example", "listing", "csv_example" + pipeline, + "jsonl_example", + "parquet_example", + "listing", + "csv_example", + "csv_duckdb_example", ) == { "jsonl_example": 1034, "parquet_example": 1034, - "listing": 10, - "csv_example": 1270, + "listing": 11, + "csv_example": 1279, + "csv_duckdb_example": 1280, } # print(pipeline.last_trace.last_normalize_info) # print(pipeline.default_schema.to_pretty_yaml())