BBMRI-ERIC Directory Scripts
September 2, 2026 ยท View on GitHub
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.