Command line tools overview

The safedata_validator package provides three main command line tools, but see also the installation documentation for tools to build local copies of the GBIF and NCBI taxonomic databases.

Resources

All of the safedata_validator command line tools require access to a shared configuration file providing validation resources and configuration information. These files are described in the configuration page and normally all of the commands on this page will automatically load your configuration data from the locations given on that page.

However, all three of the commands below also accept a manual path to a resource configuration file using --resources /path/to/file.cfg or -r /path/to/file.cfg. This can be useful, for example, if you want to have a separate configuration set up to use the Zenodo sandbox for checking your publication process. If you want to check the contents of a resources file, then all three commands also accept the --show-resources or -s option, which will validate the resources and then print a summary to screen.

safedata_validate

This tool is simply used to validate a dataset that is in the safedata format. The tool needs some simple configuration, but is intended to be fairly easy to set up and use.

For more details, see here.

safedata_zenodo

These tools are used to manage the process of publishing a validated dataset to Zenodo. The configuration is a little more complex, as it requires the setup of a Zenodo community account and access tokens.

For more details, see here.

safedata_metadata

These tools are used to manage the updating an instance of the safedata metadata server, including adding the details of published datasets and configuring core data such as the gazetteer. The configuration requires a URL for a server running the safedata server API and an access token for posting data to the server.

For more details, see here.