irv-datapkg 0.2.0

Helper package for irv-datapkg workflow

Infrastructure Resilience Assessment Data Packages

Standalone workflow to create national scale open-data packages from global open datasets.

Setup

Get the latest code by cloning this repository:

git clone [e-mail]:nismod/irv-datapkg.git

or

git clone https://github.com/nismod/irv-datapkg.git

Install Python and packages - suggest using micromamba:

micromamba create -f environment.yml

Activate the environment:

micromamba activate datapkg

Run

The data packages are produced using a snakemake workflow.

The workflow expects ZENODO_TOKEN, CDSAPI_KEY and CDSAPI_URL to be set as environment variables - these must be set before running any workflow steps.

If not interacting with Zenodo or the Copernicus Climate Data Store, these can be dummy strings:

echo "placeholder" > ZENODO_TOKEN
echo "https://cds-beta.climate.copernicus.eu/api" > CDSAPI_URL
echo "test" > CDSAPI_KEY

See Climate Data Store API docs and Zenodo API docs for access details.

Export from the file to the environment:

export ZENODO_TOKEN=$(cat ZENODO_TOKEN)
export CDSAPI_KEY=$(cat CDSAPI_KEY)
export CDSAPI_URL=$(cat CDSAPI_URL)

Check what will be run, if we ask for everything produced by the rule all, before running the workflow for real:

snakemake --dry-run all

Run the workflow, asking for all, using 8 cores, with verbose log messages:

snakemake --cores 8 --verbose all

Upload and publish

To publish, first create a Zenodo token, save it and export it as the ZENODO_TOKEN environment variable.

Upload a single data package:

snakemake --cores 1 zenodo/GBR.deposited

Publish (cannot be undone) either programmatically:

snakemake --cores 1 zenodo/GBR.published

Or after review online, through the Zenodo website (sandbox, live)

Post-publication

To get a quick list of DOIs from the Zenodo package json:

cat zenodo/*.deposition.json | jq '.metadata.prereserve_doi.doi'

To generate records.csv with details of published packages:

python scripts/published_metadata.py

Development Notes

In case of warnings about GDAL_DATA not being set, try running:

export GDAL_DATA=$(gdal-config --datadir)

To format the workflow definition Snakefile:

snakefmt Snakefile

To format the Python helper scripts:

black scripts

Related work

These Python libraries may be a useful place to start analysis of the data in the packages produced by this workflow:

• snkit helps clean network data
• nismod-snail is designed to help implement infrastructure exposure, damage and risk calculations

The open-gira repository contains a larger workflow for global-scale open-data infrastructure risk and resilience analysis.

Acknowledgments

MIT License, Copyright (c) 2023 Tom Russell and irv-datapkg contributors

This research received funding from the FCDO Climate Compatible Growth Programme. The views expressed here do not necessarily reflect the UK government's official policies.