Developer Guide

Adding support for a new NCBI database

• Implement an EutilsParserInterface

• Add the interface to EutilsXMLParserFactory

• Create a formatter extending EutilsFormatter for displaying previews to the user.

• Create a repository extending EutilsRepository for inserting into Chado.

• Add the formatter and repository to their respective factory classes.

• Add the database to the tripal_eutils_import.form.inc database list.

• Modify tripal_eutils.install, inserting any new databases necessary for the cross references. Also be sure to insert any new cvterms your repository will need.

Code Documentation:

• Connecting to NCBI: Eutils
• Formatters
  • EUtilsFormatter
  • EUtilsFormatterFactory
  • EUtilsAssemblyFormatter
  • EUtilsBioProjectFormatter
  • EUtilsBioSampleFormatter
  • EUtilsPubmedFormatter
• Repositories
  • EUtilsRepository
  • EUtilsRepositoryFactory
  • EUtilsAssemblyRepository
  • EUtilsBioProjectRepository
  • EUtilsBioSampleRepository
  • EUtilsPubmedRepository
• XML Parsers
  • EUtilsXMLParserFactory
  • EUtilsAssemblyParser
  • EUtilsBioProjectParser
  • EUtilsBioSampleParser
  • EUtilsPubmedParser