CollectionBatchTool

CollectionBatchTool is a Python library for importing, exporting, and updating batches of collection data in Specify. The intended audience is advanced users such as data managers, migration specialists, and system administrators.

• Built on top of the packages peewee and pandas
• Fast uploading of large datasets
• Requires no prior knowledge in SQL and little knowledge of Python

Source repository: https://github.com/jmenglund/CollectionBatchTool

New to CollectionBatchTool? Here are a few documents to help you get started:

• Quickstart guide – covers the most basic stuff and will take you about 10 minutes to go through.
• Preparing CSV files – explains how to prepare files for data import.
• Supported Specify Tables – lists the database tables currently supported.

Important

The current version of CollectionBatchTool (0.1.6) only supports Python 3.

Project background

CollectionBatchTool has been developed within the DINA-project in order to support migration of large datasets (100,000+ records) to Specify. The tool was first released in September 2015.

Contents

• Installing CollectionBatchTool
• Quickstart
  • Before you begin
  • Setting up the database connection
  • Exporting data from a single table
  • Importing data to a single table
  • Updating existing database records
• Advanced Operations
  • Exporting data from multiple tables
  • Importing data to multiple tables
  • Counting database records
• Preparing CSV files
  • SourceID-columns
  • Which fields are available?
• Supported Specify Tables
• API Reference
  • Module-level functions
  • The TableDataset class
  • The TreeDataset class
  • TableDataset subclasses

Indices and tables

• Index
• Module Index
• Search Page