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Datatractor Beam:
Reference implementation of the Datatractor API

Documentation Github status

Repository containing the reference implementation of the Datatractor API, published at Datatractor Yard.

For more information, see the preprint:

Datatractor: Metadata, automation, and registries for extractor interoperability in the chemical and materials sciences
Matthew L. Evans, Gian-Marco Rignanese, David Elbert & Peter Kraus
arXiv:2410.18839 (2024)

datatractor-beam package

This repository contains a draft Python 3.10 package, located under the ./beam directory. The package can be used to:

  • query the registry of Extractors for extractors that support a given file type,
  • install those extractors in a fresh Python virtual environment environment via pip,
  • invoke the extractor either in Python or at the CLI, producing Python objects or files on disk.

Installation

git clone [email protected]:datatractor/beam.git
cd beam
pip install .

Usage

Currently, you can use the extract function from the beam module inside your own Python code:

from beam import extract

# extract(<input_type>, <input_path>)
data = extract("./example.mpr",  "biologic-mpr")

This example will install the first compatible biologic-mpr extractor it finds in the registry into a fresh virtualenv (under ./beam-venvs), and then execute it on the file at example.mpr.

By default, the extract function will attempt to use the extractor's Python-based invocation (i.e. the optional preferred_mode="python" argument is specified). This means the extractor will be executed from within python, and the returned data object will be a Python object as defined (and supported) by the extractor. This may require additional packages to be installed, for examples pandas or xarray, which are both supported via the installation command pip install .[formats] above. If you encounter the following traceback, a missing "format" (such as xarray here) is the likely reason:

Traceback (most recent call last):
    [...]
    data = pickle.loads(shm.buf)
ModuleNotFoundError: No module named 'xarray'

Alternatively, if the preferred_mode="cli" argument is specified, the extractor will be executed using its command-line invocation. This means the output of the extractor will most likely be a file, which can be further specified using the output_type argument:

from beam import extract
ret = extract("example.mpr", "biologic-mpr", output_path="output.nc", preferred_mode = "cli")

In this case, the ret will be empty bytes, and the output of the extractor should appear in the output.nc file.

Finally, beam can also be executed from the command line, implying preferred_mode="cli". The command line invocation equivalent to the above Python syntax is:

beam biologic-mpr example.mpr --outfile output.nc

Plans

  • Isolation of extractor environments
    • By installing each extractor into a fresh virtualenv, multiple extractors can be installed with possibly complex (and non-Python) dependencies.
    • This could be achieved by Python virtualenvs or Docker containers (or both!).
    • This will involve setting up a system for checking locally which extractors are available on a given machine.
    • Returning Python objects in memory will be tricker in this case, and would probably require choosing a few "blessed" formats that can be passed across subprocesses without any extractor specific classes, e.g., raw JSON/Python dicts, pandas dataframes or xarray datasets (as optional requirements, by demand).
  • A command-line for quickly running e.g., beam <filename>
  • Extractor scaffold/template/plugin
    • If it can be kept similarly low-dependency, this package could also implement an extractor scaffold for those who want to modify existing extractors to follow the Datatractor API, and could automatically generate the appropriate registry entries for them.
  • Testing and validation
    • We would like to move towards output validation, and this package would be the natural place to do so, again, perhaps supporting a few blessed formats, e.g., validating JSON output against an extractor-provided JSONSchema.
    • A testing mode that runs an extractor against all example files in the registry for that file type.
  • File type detection following any rules added to the schemas
  • Support for parallel processing
    • This package could handle invoking the same extractor on a large number of files.
  • Support for other installation methods, such as conda and docker, to expand beyond purely pip-installable extractors.