From 115a695a16e6a94767ec6058fe9ed9588e694e56 Mon Sep 17 00:00:00 2001 From: Ceceliachenen <162673161+Ceceliachenen@users.noreply.github.com> Date: Wed, 5 Jun 2024 19:48:55 +0800 Subject: [PATCH] Add tabular reader (#47) * tabular reader * tabular reader * tabular reader * tabular reader * tabular reader * tabular reader --------- Co-authored-by: Yue Fei <59813791+moria97@users.noreply.github.com> --- poetry.lock | 244 ++++++++++-------- pyproject.toml | 1 + src/pai_rag/docs/tabular_doc.md | 76 ++++++ .../integrations/readers/pai_csv_reader.py | 151 +++++++++++ .../integrations/readers/pai_excel_reader.py | 121 +++++++++ .../modules/datareader/datareader_factory.py | 11 + tests/data_readers/test_csv_reader.py | 48 ++++ tests/data_readers/test_excel_reader.py | 32 +++ ...45\255\230\347\216\207_csv_two_header.csv" | 9 + ...255\230\347\216\207_excel_two_header.xlsx" | Bin 0 -> 9147 bytes 10 files changed, 579 insertions(+), 114 deletions(-) create mode 100644 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for developers to extract data from Microsoft Excel (tm) .xls spreadsheet files" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +files = [ + {file = "xlrd-2.0.1-py2.py3-none-any.whl", hash = "sha256:6a33ee89877bd9abc1158129f6e94be74e2679636b8a205b43b85206c3f0bbdd"}, + {file = "xlrd-2.0.1.tar.gz", hash = "sha256:f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88"}, +] + +[package.extras] +build = ["twine", "wheel"] +docs = ["sphinx"] +test = ["pytest", "pytest-cov"] + [[package]] name = "xxhash" version = "3.4.1" @@ -7839,4 +7855,4 @@ test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-it [metadata] lock-version = "2.0" python-versions = ">=3.10.0,<3.12" -content-hash = "5c891b42861023d77d87bf4027b2b3e53fe7eaad67d81c893f7f5be7e45a8e69" +content-hash = "efc14eedd786e12d84883e0b2dd2319a4b538a1a88891d995cd4c3fde14da2c3" diff --git a/pyproject.toml b/pyproject.toml index 5398cebc..aa7ce73b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -69,6 +69,7 @@ openinference-instrumentation = "^0.1.7" llama-index-llms-huggingface = "^0.2.0" pytest-asyncio = "^0.23.7" pytest-cov = "^5.0.0" +xlrd = "^2.0.1" [tool.poetry.scripts] pai_rag = "pai_rag.main:main" diff --git a/src/pai_rag/docs/tabular_doc.md b/src/pai_rag/docs/tabular_doc.md new file mode 100644 index 00000000..8791cf64 --- /dev/null +++ b/src/pai_rag/docs/tabular_doc.md @@ -0,0 +1,76 @@ +# Tabular processing with PAI-RAG + +## PaiCSVReader + +PaiCSVReader(concat_rows=True, row_joiner="\n", csv_config={}) + +### Parameters: + +**concat_rows:** _bool, default=True._ +Whether to concatenate rows into one document. + +**row_joiner:** _str, default="\n"._ +The separator used to join rows. + +**header:** _None or int, list of int, default 0._ +row (0-indexed) to use for the column labels of the parsed DataFrame. If a list of integers is passed those row +positions will be combined into a MultiIndex. Use None if there is no header. + +### Functions: + +load_data(file: Path, extra_info: Optional[Dict] = None, fs: Optional[AbstractFileSystem] = None) + +## PaiPandasCSVReader + +PaiPandasCSVReader(concat_rows=True, row_joiner="\n", pandas_config={}) + +### Parameters: + +**concat_rows:** _bool, default=True._ +Whether to concatenate rows into one document. + +**row_joiner:** _str, default="\n"._ +The separator used to join rows. + +**pandas_config:** _dict, default={}._ +The configuration of pandas.read_csv. +Refer to https://pandas.pydata.org/docs/reference/api/pandas.read_csv.html for more information. +Set to empty dict by default, this means pandas will try to figure out the separators, table head, etc. on its own. + +#### one important parameter: + +**header:** _None or int, list of int, default 0._ +Row (0-indexed) to use for the column labels of the parsed DataFrame. If a list of integers is passed those row +positions will be combined into a MultiIndex. Use None if there is no header. + +### Functions: + +load_data(file: Path, extra_info: Optional[Dict] = None, fs: Optional[AbstractFileSystem] = None) + +## PaiPandasExcelReader + +PaiPandasExcelReader(concat_rows=True, row_joiner="\n", pandas_config={}) + +### Parameters: + +**concat_rows:** _bool, default=True._ +Whether to concatenate rows into one document. + +**row_joiner:** _str, default="\n"._ +The separator used to join rows. + +**pandas_config:** _dict, default={}._ +The configuration of pandas.read_csv. +Refer to https://pandas.pydata.org/docs/reference/api/pandas.read_excel.html for more information. +Set to empty dict by default, this means pandas will try to figure out the separators, table head, etc. on its own. + +#### one important parameter: + +**header:** _None or int, list of int, default 0._ +Row (0-indexed) to use for the column labels of the parsed DataFrame. If a list of integers is passed those row +positions will be combined into a MultiIndex. Use None if there is no header. + +### Functions: + +load_data(file: Path, extra_info: Optional[Dict] = None, fs: Optional[AbstractFileSystem] = None) +only process the first sheet diff --git a/src/pai_rag/integrations/readers/pai_csv_reader.py b/src/pai_rag/integrations/readers/pai_csv_reader.py new file mode 100644 index 00000000..3d1bde60 --- /dev/null +++ b/src/pai_rag/integrations/readers/pai_csv_reader.py @@ -0,0 +1,151 @@ +"""Tabular parser-CSV parser. + +Contains parsers for tabular data files. + +""" + +from pathlib import Path +from typing import Any, Dict, List, Optional +from fsspec import AbstractFileSystem + +import pandas as pd +from llama_index.core.readers.base import BaseReader +from llama_index.core.schema import Document + + +class PaiCSVReader(BaseReader): + """CSV parser. + + Args: + concat_rows (bool): whether to concatenate all rows into one document. + If set to False, a Document will be created for each row. + True by default. + header （object）: None or int, list of int, default 0. + Row (0-indexed) to use for the column labels of the parsed DataFrame. If a list of integers is passed those row + positions will be combined into a MultiIndex. Use None if there is no header. + + """ + + def __init__( + self, *args: Any, concat_rows: bool = True, header: object = 0, **kwargs: Any + ) -> None: + """Init params.""" + super().__init__(*args, **kwargs) + self._concat_rows = concat_rows + self._header = header + + def load_data( + self, file: Path, extra_info: Optional[Dict] = None + ) -> List[Document]: + """Parse csv file. + + Returns: + Union[str, List[str]]: a string or a List of strings. + + """ + try: + import csv + except ImportError: + raise ImportError("csv module is required to read CSV files.") + text_list = [] + headers = [] + data_lines = [] + data_line_start_index = 1 + if isinstance(self._header, list): + data_line_start_index = max(self._header) + 1 + elif isinstance(self._header, int): + data_line_start_index = self._header + 1 + self._header = [self._header] + + with open(file) as fp: + csv_reader = csv.reader(fp) + + if self._header is None: + for row in csv_reader: + text_list.append(", ".join(row)) + else: + for i, row in enumerate(csv_reader): + if i in self._header: + headers.append(row) + elif i >= data_line_start_index: + data_lines.append(row) + headers = [tuple(group) for group in zip(*headers)] + for line in data_lines: + if len(line) == len(headers): + data_entry = str(dict(zip(headers, line))) + text_list.append(data_entry) + + metadata = {"filename": file.name, "extension": file.suffix} + if extra_info: + metadata = {**metadata, **extra_info} + + if self._concat_rows: + return [Document(text="\n".join(text_list), metadata=metadata)] + else: + return [Document(text=text, metadata=metadata) for text in text_list] + + +class PaiPandasCSVReader(BaseReader): + r"""Pandas-based CSV parser. + + Parses CSVs using the separator detection from Pandas `read_csv`function. + If special parameters are required, use the `pandas_config` dict. + + Args: + concat_rows (bool): whether to concatenate all rows into one document. + If set to False, a Document will be created for each row. + True by default. + + row_joiner (str): Separator to use for joining each row. + Only used when `concat_rows=True`. + Set to "\n" by default. + + pandas_config (dict): Options for the `pandas.read_csv` function call. + Refer to https://pandas.pydata.org/docs/reference/api/pandas.read_csv.html + for more information. + Set to empty dict by default, this means pandas will try to figure + out the separators, table head, etc. on its own. + + """ + + def __init__( + self, + *args: Any, + concat_rows: bool = True, + row_joiner: str = "\n", + pandas_config: dict = {}, + **kwargs: Any + ) -> None: + """Init params.""" + super().__init__(*args, **kwargs) + self._concat_rows = concat_rows + self._row_joiner = row_joiner + self._pandas_config = pandas_config + + def load_data( + self, + file: Path, + extra_info: Optional[Dict] = None, + fs: Optional[AbstractFileSystem] = None, + ) -> List[Document]: + """Parse csv file.""" + if fs: + with fs.open(file) as f: + df = pd.read_csv(f, **self._pandas_config) + else: + df = pd.read_csv(file, **self._pandas_config) + + text_list = df.apply( + lambda row: str(dict(zip(df.columns, row.astype(str)))), axis=1 + ).tolist() + + if self._concat_rows: + return [ + Document( + text=(self._row_joiner).join(text_list), metadata=extra_info or {} + ) + ] + else: + return [ + Document(text=text, metadata=extra_info or {}) for text in text_list + ] diff --git a/src/pai_rag/integrations/readers/pai_excel_reader.py b/src/pai_rag/integrations/readers/pai_excel_reader.py new file mode 100644 index 00000000..c300985a --- /dev/null +++ b/src/pai_rag/integrations/readers/pai_excel_reader.py @@ -0,0 +1,121 @@ +"""Tabular parser-Excel parser. + +Contains parsers for tabular data files. + +""" + +from pathlib import Path +from typing import Any, Dict, List, Optional +from fsspec import AbstractFileSystem +from openpyxl import load_workbook + +import pandas as pd +from llama_index.core.readers.base import BaseReader +from llama_index.core.schema import Document + + +class PaiPandasExcelReader(BaseReader): + r"""Pandas-based Excel parser. + + + Args: + concat_rows (bool): whether to concatenate all rows into one document. + If set to False, a Document will be created for each row. + True by default. + + row_joiner (str): Separator to use for joining each row. + Only used when `concat_rows=True`. + Set to "\n" by default. + + pandas_config (dict): Options for the `pandas.read_excel` function call. + Refer to https://pandas.pydata.org/docs/reference/api/pandas.read_excel.html + for more information. + Set to empty dict by default, this means pandas will try to figure + out the separators, table head, etc. on its own. + + """ + + def __init__( + self, + *args: Any, + concat_rows: bool = True, + row_joiner: str = "\n", + pandas_config: dict = {}, + **kwargs: Any + ) -> None: + """Init params.""" + super().__init__(*args, **kwargs) + self._concat_rows = concat_rows + self._row_joiner = row_joiner + self._pandas_config = pandas_config + + def read_xlsx( + self, + file: Path, + fs: Optional[AbstractFileSystem] = None, + ): + """Parse Excel file。""" + if fs: + with fs.open(file) as f: + excel = pd.ExcelFile(load_workbook(f), engine="openpyxl") + else: + excel = pd.ExcelFile(load_workbook(file), engine="openpyxl") + sheet_name = excel.sheet_names[0] + sheet = excel.book[sheet_name] + df = excel.parse(sheet_name, **self._pandas_config) + + header_max = 0 + if ( + "header" in self._pandas_config + and self._pandas_config["header"] is not None + and isinstance(self._pandas_config["header"], list) + ): + header_max = max(self._pandas_config["header"]) + elif ( + "header" in self._pandas_config + and self._pandas_config["header"] is not None + and isinstance(self._pandas_config["header"], int) + ): + header_max = self._pandas_config["header"] + + for item in sheet.merged_cells: + top_col, top_row, bottom_col, bottom_row = item.bounds + base_value = item.start_cell.value + # Convert 1-based index to 0-based index + top_row -= 1 + top_col -= 1 + # Since the previous lines are set as headers, the coordinates need to be adjusted here. + if ( + "header" in self._pandas_config + and self._pandas_config["header"] is not None + ) or "header" not in self._pandas_config: + top_row -= header_max + 1 + bottom_row -= header_max + 1 + + df.iloc[top_row:bottom_row, top_col:bottom_col] = base_value + return df + + def load_data( + self, + file: Path, + extra_info: Optional[Dict] = None, + fs: Optional[AbstractFileSystem] = None, + ) -> List[Document]: + """Parse Excel file. only process the first sheet""" + + df = self.read_xlsx(file, fs) + + text_list = df.apply( + lambda row: str(dict(zip(df.columns, row.astype(str)))), axis=1 + ).tolist() + + if self._concat_rows: + return [ + Document( + text=(self._row_joiner).join(text_list), metadata=extra_info or {} + ) + ] + else: + return [ + Document(text=text, metadata=extra_info or {}) for text in text_list + ] diff --git a/src/pai_rag/modules/datareader/datareader_factory.py b/src/pai_rag/modules/datareader/datareader_factory.py index abb46105..8c0b0c60 100644 --- a/src/pai_rag/modules/datareader/datareader_factory.py +++ b/src/pai_rag/modules/datareader/datareader_factory.py @@ -4,6 +4,8 @@ from pai_rag.integrations.readers.pai_pdf_reader import PaiPDFReader from pai_rag.integrations.readers.llama_parse_reader import LlamaParseDirectoryReader from pai_rag.integrations.readers.html.html_reader import HtmlReader +from pai_rag.integrations.readers.pai_csv_reader import PaiPandasCSVReader +from pai_rag.integrations.readers.pai_excel_reader import PaiPandasExcelReader from llama_index.readers.database import DatabaseReader from llama_index.core import SimpleDirectoryReader import logging @@ -25,6 +27,15 @@ def _create_new_instance(self, new_params: Dict[str, Any]): enable_image_ocr=self.reader_config.get("enable_image_ocr", False), model_dir=self.reader_config.get("easyocr_model_dir", None), ), + ".csv": PaiPandasCSVReader( + concat_rows=self.reader_config.get("concat_rows", False), + ), + ".xlsx": PaiPandasExcelReader( + concat_rows=self.reader_config.get("concat_rows", False), + ), + ".xls": PaiPandasExcelReader( + concat_rows=self.reader_config.get("concat_rows", False), + ), } return self diff --git a/tests/data_readers/test_csv_reader.py b/tests/data_readers/test_csv_reader.py new file mode 100644 index 00000000..f3de5b14 --- /dev/null +++ b/tests/data_readers/test_csv_reader.py @@ -0,0 +1,48 @@ +import os +from pathlib import Path +from pai_rag.core.rag_configuration import RagConfiguration +from pai_rag.modules.module_registry import module_registry +from pai_rag.integrations.readers.pai_csv_reader import PaiCSVReader, PaiPandasCSVReader +from llama_index.core import SimpleDirectoryReader + +BASE_DIR = Path(__file__).parent.parent.parent + + +def test_csv_reader(): + config_file = os.path.join(BASE_DIR, "src/pai_rag/config/settings.toml") + config = RagConfiguration.from_file(config_file).get_value() + module_registry.init_modules(config) + reader_config = config["data_reader"] + directory_reader = SimpleDirectoryReader( + input_dir="tests/testdata/data/csv_data", + file_extractor={ + ".csv": PaiCSVReader( + concat_rows=reader_config.get("concat_rows", False), + header=[0, 1], + ) + }, + ) + documents = directory_reader.load_data() + for doc in documents: + print(doc) + assert len(documents) == 7 + + +def test_pandas_csv_reader(): + config_file = os.path.join(BASE_DIR, "src/pai_rag/config/settings.toml") + config = RagConfiguration.from_file(config_file).get_value() + module_registry.init_modules(config) + reader_config = config["data_reader"] + directory_reader = SimpleDirectoryReader( + input_dir="tests/testdata/data/csv_data", + file_extractor={ + ".csv": PaiPandasCSVReader( + concat_rows=reader_config.get("concat_rows", False), + pandas_config={"header": [0, 1]}, + ) + }, + ) + documents = directory_reader.load_data() + for doc in documents: + print(doc) + assert len(documents) == 7 diff --git a/tests/data_readers/test_excel_reader.py b/tests/data_readers/test_excel_reader.py new file mode 100644 index 00000000..c98aad42 --- /dev/null +++ b/tests/data_readers/test_excel_reader.py @@ -0,0 +1,32 @@ +import os +from pathlib import Path +from pai_rag.core.rag_configuration import RagConfiguration +from pai_rag.modules.module_registry import module_registry +from pai_rag.integrations.readers.pai_excel_reader import PaiPandasExcelReader +from llama_index.core import SimpleDirectoryReader + +BASE_DIR = Path(__file__).parent.parent.parent + + +def test_pandas_excel_reader(): + config_file = os.path.join(BASE_DIR, "src/pai_rag/config/settings.toml") + config = RagConfiguration.from_file(config_file).get_value() + module_registry.init_modules(config) + reader_config = config["data_reader"] + directory_reader = SimpleDirectoryReader( + input_dir="tests/testdata/data/excel_data", + file_extractor={ + ".xlsx": PaiPandasExcelReader( + concat_rows=reader_config.get("concat_rows", False), + pandas_config={"header": [0, 1]}, + ), + ".xls": PaiPandasExcelReader( + concat_rows=reader_config.get("concat_rows", False), + pandas_config={"header": [0, 1]}, + ), + }, + ) + documents = directory_reader.load_data() + for doc in documents: + print(doc) + assert len(documents) == 7 diff --git "a/tests/testdata/data/csv_data/30\345\244\251\347\225\231\345\255\230\347\216\207_csv_two_header.csv" "b/tests/testdata/data/csv_data/30\345\244\251\347\225\231\345\255\230\347\216\207_csv_two_header.csv" new file mode 100644 index 00000000..b0585488 --- /dev/null +++ "b/tests/testdata/data/csv_data/30\345\244\251\347\225\231\345\255\230\347\216\207_csv_two_header.csv" @@ -0,0 +1,9 @@ +time,metric +date,rate +20240101,0.9375 +20240201,0.9744 +20240301,0.9767 +20240401,0.9375 +20240501,0.9091 +20240601,0.9474 +20240701,0.9667 \ No newline at end of file diff --git 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