Bidirectional conversion between JSON(-LD) and iRODS AVUs

Rationale

JSON is a flexible and easy to use format for storing (nested) data. At the same time it can remain human readable. It can therefore be an ideal method for storing metadata in iRODS. However, iRODS uses Attribute, Value, Unit triples. Its largest drawback being the lack of nesting.

This Python module describes a method for converting JSON to AVU triples and back again (bidirectional).

Design goals

• Bijection between JSON <-> AVU
  • i.e no limit on the characters used in an attribute
  • i.e being able to maintain order in arrays
• Lean JSON -> AVU conversion.
  • Don't explode the JSON unnecessarily in AVUs
• Keep Attribute->Value pairs the same in JSON and AVUs. So values remain easily accessible from within iRODS
• Compatible with existing or additional AVUs
• Compatible/aware of JSON-LD
• Unicode-safe

Implementation

The unit is field is being used for the following purposes:

1. The JSON-AVU namespace
2. The parent object (0 by default)
3. The object type (o, s, b, a, n, z, e)
4. The array index

AVUs only allow a string value. The types are converted as follows:

• s: string
• o: object ("o" + object_id)
• b: boolean ("True" or "False")
• n: number (String value of float or int)
• z: null (".")
• e: empty string (".") (special case as AVUs don't allow empty values)
• a: empty array (".")

Installation

Either clone the git repository, or use pip to install the module into your Python (virtual) environment:

pip install irods_avu_json

From within iRODS

This Python module, by itself, has no interaction or awareness of iRODS.

There is a companion repository irods_avu_json-ruleset that contains all the iRODS rules, policies, and microservices to make the conversion code operational in iRODS.

Docker

A description of a docker container running the ruleset, its microservices, and python dependencies exists in the irods_avu_json-docker repository. You can use this to quickly try out this module and test its functionality.

Example output

Source:
{
    "k1": "v1",
    "k2": {
        "k3": "v2",
        "k4": "v3"
    },
    "k5": [
        "v4",
        "v5"
    ],
    "k6": [
        {
            "k7": "v6",
            "k8": "v7"
        }
    ]
}
AVUs:
      A       V               U
     k1      v1        root_0_s
     k2      o1       root_0_o1
     k3      v2        root_1_s
     k4      v3        root_1_s
     k5      v4      root_0_s#0
     k5      v5      root_0_s#1
     k6      o2     root_0_o2#0
     k7      v6        root_2_s
     k8      v7        root_2_s
JSON:
{
    "k1": "v1",
    "k2": {
        "k3": "v2",
        "k4": "v3"
    },
    "k5": [
        "v4",
        "v5"
    ],
    "k6": [
        {
            "k7": "v6",
            "k8": "v7"
        }
    ]
}

Development helpers

Use the conversion.py script for easy development. Compatible with Python 2 and 3.

python conversion.py inputs/basic.json

Testing

Tests can be run from the top-level directory (requires Python3).

python3 -m unittest test

Limits

On the AVU side

• If two AVUs have the same attribute and unit but different values only the last one ends up in the JSON

More information

This work was presented at the iRODS UGM2019 in Utrecht, The Netherlands. You can view the recording, the slides or the accompying paper for more information.

Authors

Paul van Schayck ([email protected]), Ton Smeele, Daniel Theunissen and Lazlo Westerhof

Copyright and license

(c) Maastricht University (c) Utrecht University

Apache License 2.0