BBMRI-ERIC Directory Scripts

This repository contains the BBMRI-ERIC Directory data-quality checker and a collection of exporters, reports, map generators, maintenance tools, analyses, and reusable Python libraries built around the Directory.

The original and primary entry point is the data-quality checker:

python3 data-check.py

Quick Start

pip3 install -r requirements.txt
python3 data-check.py

For authentication, cache behavior, Python compatibility, and common command line options, see Setup and common operation.

Tool Families

Family	Main entry points	Documentation
Data quality	data-check.py, checks/, qcheck-updater.py	Data quality
Exports and reports	exporter-*.py	Exporters
Maps and geospatial output	geocoding_2022.py, R-maps/	Maps
Data maintenance and synchronization	directory-tables-modifier.py, updater/importer/sync tools	Maintenance tools
Auxiliary analyses and utilities	survey-so2-directory.py, search, statistics, conversion helpers	Auxiliary tools
Reusable Python modules	directory.py and focused helper modules	Libraries

Common Examples

Run the default quality checks and write an XLSX report:

python3 data-check.py -X results.xlsx

Export the main Directory entities:

python3 exporter-all.py -X directory.xlsx

Generate the GeoJSON used by the map framework:

python3 geocoding_2022.py geocoding.config -o bbmri-directory-geojson

Every CLI provides its authoritative option list through -h or --help.

Documentation Model

• docs/ is user-facing documentation: installation, commands, inputs, outputs, examples, and operational safety warnings.
• DEVELOPMENT.md contains architecture and detailed functionality specifications for maintainers.
• AGENTS.md contains concise, non-negotiable implementation guardrails derived from those specifications.
• R-maps/README.md contains the detailed R map workflow.

User documentation explains how to operate the current implementation. It is not the canonical location for internal behavioral contracts.

Development

Install test dependencies and run the suite:

pip3 install -r requirements-test.txt
pytest -q

See DEVELOPMENT.md for architecture, module boundaries, testing expectations, and functionality specifications.