h5ld: HDF5 Linked Data

Linked Data are becoming more popular for user-created metadata in HDF5 files. This Python package provides readers for the HDF5-based formats with such metadata . Entire linked data content is read in one operation and made available as an rdflib graph object.

Currently supported:

• Allotrope Data Format (ADF)

Installation

pip install git+https://github.com/HDFGroup/h5ld@{LABEL}

where {LABEL} is either master or a tag label.

Requirements:

• Python >= 3.7
• h5py >= 3.3.0
• rdflib >= 5.0.0

License

This software is open source. See this file for details.

Quick Start

This package can be used either as a command-line tool or programmatically. On the command-line, the package dumps the link data of an input HDF5 file into several popular RDF formats supported by the rdflib package. For example:

python -m h5ld -f json-ld -o output.json INPUT.h5

will dump the input file's RDF data to a file output.json in the JSON-LD format. Omitting an output file prints out the same content so it can be ingested by another command-line tool. Full description is available from:

python -m h5ld --help

There is also a programmatic interface for integration into Python applications. Each h5ld reader will provide the following methods and attributes:

• File format name.

  print(f"Input file format is: {reader.name}")

• Short (usually an acronym) of the file format.

  print(f"File format acronym: {reader.short_name}")

• Check if the reader is the right choice for the input file.

  with h5py.File("input.h5", mode="r") as f:
      if reader.verify_format(f):
          # Do something...
        else:
            print("Sorry but not the right h5ld reader.")

• Check if there is linked data content in the input HDF5 file. Optionally, print an appropriate description of the data.

  with h5py.File("input.h5", mode="r") as f:
      reader.check_ld(f, report=True)

• Read linked data and export it to a destination in the requested RDF format.

  with h5py.File("input.h5", mode="r") as f:
      reader(f).dump_ld("output.json", format="json-ld")

• Read linked data and return either an rdflib.Graph or rdflib.ConjunctiveGraph object.

  with h5py.File("input.h5", mode="r") as f:
      graph = reader(f).get_ld()

• A Python dictionary with the reader's namespace prefixes and their IRIs.

  with h5py.File("input.h5", mode="r") as f:
      rdr = reader(f)
      namespaces = rdr.namespaces