Add utilities to shard CSV/MCF files

[ajaits]

Adds the following utilities to shard csv and mcf files:

• file_dict_io.py: Class to read/write dict records from CSv/MCF files.
• file_sharder.py: Utility to deterministically shard files using a key that can be a combination of properties.

This can be used to generate shards of smaller MCF files for differ or dc-import genmcf.
Using a key that groups observations by "{observationAbout}{variableMeasured}" allows stats checks for duplicate observations and time series holes with genmcf on a single csv shard.

For example, to shard processed CSVs for the next stages of file-wise genmcf and differ:
python file_sharder.py --shard_input=output/*.csv --shard_output=shard/[email protected] --shard_key="{observationAbout}{variableMeasured}"

This generates smaller files of the form shard/sharded-output-0000?-of-00010.csv that can be passed individually to
genmcf and differ.

[gemini-code-assist]

Summary of Changes

Hello @ajaits, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request introduces a robust set of utilities for sharding large CSV and MCF (McfFile) files. It provides a flexible framework to read and write dictionary-like data from these file types and then distribute records into multiple smaller files based on a configurable sharding key, offering features like duplicate handling and sampling.

Highlights

• New File I/O Abstraction: Introduced FileDictIO as an abstract base class, with concrete implementations CsvFileDictIO and McfFileDictIO, enabling standardized reading and writing of data records as dictionaries from CSV and MCF files.
• Comprehensive File Sharder: Developed FileSharder and a shard_file function that leverages the new FileDictIO classes to efficiently shard input files. It supports specifying a sharding key (e.g., a column name or property), determining shard counts dynamically, skipping duplicate records, and sampling input data.
• Enhanced File Utility: The FileIO class in file_util.py now exposes a get_file_handle method, which is utilized by the new FileDictIO classes.
• Improved Flag Parsing: A minor but important fix in mcf_diff.py ensures that absl.flags are properly parsed before accessing flag values, preventing potential runtime errors.
• Dedicated Test Coverage: New unit tests (file_dict_io_test.py and file_sharder_test.py) have been added to validate the functionality and correctness of the new file I/O and sharding utilities.

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[gemini-code-assist]

Code Review

This pull request introduces new utilities for sharding CSV and MCF files, a significant piece of new functionality. The implementation includes I/O helpers in file_dict_io.py and the main sharding logic in file_sharder.py, along with unit tests. The code is generally well-structured. However, I've identified a few issues that should be addressed, including potential runtime errors like an AttributeError from an uninitialized variable and a ZeroDivisionError. There are also some opportunities to improve code clarity and address module dependency issues related to sys.path manipulation.

[gemini-code-assist]

The indentation of the closing brace } is incorrect. It is indented by 6 spaces, while the return statement is at 4 spaces. For consistency and to fix the formatting, it should be aligned with the return statement at 4 spaces.

Suggested change

	}
	}

[gemini-code-assist]

The __next__ method is already defined in the base class FileDictIO to call self.next(). Redefining it in the subclass CsvFileDictIO with the exact same implementation is redundant. This method can be removed from the subclass.

[gemini-code-assist]

The __next__ method is already defined in the base class FileDictIO to call self.next(). Redefining it in the subclass McfFileDictIO with the exact same implementation is redundant. This method can be removed from the subclass.