Tripal Developer Toolkit

Abstract

Tripal community database construction toolkit utilizing the content management system Drupal. Tripal is used to make biological, genetic and genomic data more discoverable, shareable, searchable and standardized. As funding for community-level genomics databases declines, Tripal's open-source codebase provides a means for sites to be built and maintained with a minimal investment in staff and new development. Tripal is ultimately as strong as the community of sites and developers that use it. We present a set of developer tools that will make building and maintaining Tripal 3 sites easier for new and returning users. These tools break down barriers to entry such as setting up developer and testing environments, acquiring and loading test datasets, working with controlled vocabulary terms and writing new Drupal classes.

Figure 1

The Tripal Alchemist administrator tool. The Tripal Alchemist administrator interface. To convert entities, the administrator must first select a transformation method (top). In this example, choosing the manual method allows conversion of selected entities from a source type to a destination type (middle). The available source entities are then presented in a table (bottom), which the user can select from and submit.

Figure 2

Input and output for TFG. The command line program prompts the user to provide a series of inputs (A) and checks the database to determine if the specified controlled vocabulary term exists. If it does, the software produces a set of files in the correct directory structure to generate the field (B). An example is given using the ‘Geographic location’ term from the Gazetteer vocabulary for a mock module named Tripal_Biosample (C). This demonstrates how the user’s inputs are structured into the file names. These inputs are also used to build all the necessary code variables and functions in each file, leaving only the essential custom coding for the function bodies for the developer to finish.