naan_reg_public

This is a public representation of the information contained in the private NAAN registry records.

The content is expressed in JSON and is generated using a python script executed by a GitHub action that retrieves the current copy of the main_naans file from the NAAN registry, parses the ANVL, and generates the JSON records as a single JSON document and also as a folder hierarchy of individual JSON records.

The artifacts are published using GitHub pages, accessible at:

https://cdluc3.github.io/naan_reg_public/

The conversion script

naan_reg_json provides a tool for converting NAAN registry ANVL to JSON. It includes JSON-schema with generated documentation for private and publicly visible NAAN records.

Usage

$python naan_reg_json.py --help
usage: naan_reg_json.py [-h] [-p] [path]

Generate JSON representation of naan_reg_priv/main_naans. This tool translates the 
NAAN registry file from ANVL to JSON to assist downstream programmatic use. If pydantic 
is installed then the script can output JSON schema describing the JSON respresentation 
of the transformed NAAN entries.

positional arguments:
  path          Path to naan_reg_priv ANVL file.

optional arguments:
  -h, --help    show this help message and exit
  -p, --public  Output public content only.

For conversion from ANVL to JSON no additional dependencies are needed if using Python3.8 or later. E.g. (portions redacted):

$python naan_reg_json.py ../naan_reg_priv/main_naans

{
  "12025": {
    "what": "12025",
    "where": "http://www.nlm.nih.gov",
    "target": "http://www.nlm.nih.gov/$arkpid",
    "when": "2001-03-08T00:00:00+00:00",
    "who": {
      "name": "US National Library of Medicine",
      "acronym": null,
      "address": "8600 Rockville Pike, Bethesda, MD 20894, USA"
    },
    "na_policy": {
      "orgtype": "NP",
      "policy": "(:unkn) unknown",
      "tenure": "2001",
      "policy_url": null
    },
    "test_identifier": null,
    "service_provider": null,
    "purpose": "unspecified",
    "why": "ARK",
    "contact": {
      "name": "M",
      "unit": null,
      "tenure": null,
      "email": "",
      "phone": ""
    },
    "alternate_contact": null,
    "comments": null,
    "provider": null
  },
  ...

A public view of the ANVL to JSON can be generated using the -p or --public option:

$python naan_reg_json.py -p ../naan_reg_priv/main_naans

{
  "12025":{
    "what": "12025",
    "where": "http://www.nlm.nih.gov",
    "target": "http://www.nlm.nih.gov/$arkpid",
    "when": "2001-03-08T00:00:00+00:00",
    "who": {
        "name": "US National Library of Medicine",
        "acronym": null
    },
    "na_policy": {
        "orgtype": "NP",
        "policy": "(:unkn) unknown",
        "tenure": "2001",
        "policy_url": null
    },
    "test_identifier": null,
    "service_provider": null,
    "purpose": "unspecified"
    }
  },
  ...

For JSON-schema generation, pydantic is required:

pip install pydantic

The public view and full view have different schemas, they can be generated like:

$python naan_reg_json.py -s > schema/naan_schema.json

and

$python naan_reg_json.py -s -p > schema/public/naan_schema.json

Schema documentation can be generated if json-schema-for-humans is installed:

pip install json-schema-for-humans

To generate the schema documentation:

generate-schema-doc --config-file docs_config.yaml ./schema/naan_schema.json ./schema/
generate-schema-doc --config-file docs_config.yaml --config template_name=md ./schema/naan_schema.json ./schema/
generate-schema-doc --config-file docs_config.yaml ./schema/public/naan_schema.json ./schema/public/
generate-schema-doc --config-file docs_config.yaml --config template_name=md ./schema/public/naan_schema.json ./schema/public/

Acknowledgement

This work is supported by the California Digital Library.

datadavev/naan_reg_public_fork

naan_reg_public

The conversion script

Usage

Acknowledgement