h5json Package

This package provides CLI tools for conversion between HDF5 files and HDF5/JSON, and HDF5/JSON validation.

Installation

The standard method using the pip tool is recommended:

pip install h5json

If interested in an unreleased version, install directly from the repository:

pip install git+https://github.com/HDFGroup/hdf5-json.git@{LABEL}

{LABEL} is a branch, tag, or commit identifier. pip documentation explains available install features.

For development, create a fork of the repository and execute:

$ mkdir my-h5json-dev
$ cd my-h5json-dev
$ git clone https://{MYUSERNAME}@github.com/{MYUSERNAME}/hdf5-json.git
$ cd h5json
$ pip install -e .

GitHub documentation explains this workflow in great detail.

Verification

To verify h5json was installed correctly convert an HDF5 file to HDF5/JSON and back. Run the following commands:

$ h5tojson sample.h5 > sample.json
$ h5jvalidate sample.json
$ jsontoh5 sample.json new-sample.h5

The file sample.json should contain HDF5/JSON description of the original file and the file new-sample.h5 should be an HDF5 equivalent to the original file sample.h5.

CLI Tools

The h5json distribution provides three command-line tools described below.

jsontoh5

Generate an HDF5 file with the content, storage features, and data described in an HDF5/JSON file.

Usage:

jsontoh5.py [-h] <json_file> <h5_file>

where:

<json_file>

Input HDF5/JSON file.

<h5_file>

Output HDF5 file that will be created.

Options:

-h

Print help message.

h5tojson

Convert the input HDF5 file to its HDF5/JSON representation. Output is printed to stdout.

Usage:

h5tojson [-h] [-D] [-d] <hdf5_file>

where:

<hdf5_file>

HDF5 file.

Options:

-h

Print help message.

-D

Suppress all data output. Output HDF5/JSON will not contain any dataset or attribute values.

-d

Suppress data output for datasets only.

h5jvalidate

Validate generated HDF5/JSON files against the schema. Validation errors are printed to stderr. Command’s exit status indicates the overall success (0) or failure (1).

Usage:

h5jvalidate [-h|--help] [-s|--stop] JSON_LOC [JSON_LOC ...]

where:

JSON_LOC

HDF5/JSON location (files or folders). If a folder, all files with .json extension will be selected for validation.

Options:

-s, --stop

Stop after first HDF5/JSON file failed validation (default: False)

-h, --help

Print help message.