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The safedata_validator API

The safedata_validator package is divided into submodules handling different components of the validation process.

  • The summary module handles the parsing and validation of the Summary datasheet
  • The locations module handles the loading of the locations gazetteer and providing a Locations class to be used in validation of the Locations datasheet.
  • Similarly, the taxa module handles the creation of taxonomic validation classes, using a local database to check the contents of the GBIF taxa worksheet and checking that any sequencing data is provided in a searchable format.
  • The field module contains all of the code for reading and validating data worksheets, along with the main Dataset class used to load and validate entire dataset files.
  • The resources module is used to load and validate the configuration file.
  • The extent module is used to configure and track the temporal and spatial extents of a dataset.
  • The logger module is used to set up logging of the validation process. Logging is a core component of the system, because the validation process is written to work through the whole file, logging issues as it goes, rather than exiting at the first problem.
  • The taxondb module is used to download copies of the GBIF taxonomy database and build usable local SQLite3 databases from them.
  • The zenodo module is used to communicate with the Zenodo in order to create and upload Zenodo deposits.
  • The server module is used to communicate with the metadata server in order to upload dataset metadata.
  • The utilities module contains helper functions used across the other modules