Utilities

Here live the more mundane and backend utilities used throughout other modules of the codebase, and potentially elsewhere, although they are not intended for external use in general. Several more-or-less bespoke scripts are also stored here.

Database Session Constructors (indra_db.util.constructors)

Constructors to get interfaces to the different databases, selecting among the various physical instances defined in the config file.

Scripts to Get Content (indra_db.util.content_scripts)

General scripts for getting content by various IDs.

Distilling Raw Statements (indra_db.util.distill_statements)

Do some pre-pre-assembly cleansing of the raw Statements to account for various kinds of duplicity that are artifacts of our content collection and reading pipelines rather than representing actually duplicated knowledge in the literature.

Script to Create a SIF Dump (indra_db.util.dump_sif)

Create an interactome from metadata in the database and dump the results as a sif file.

General Helper Functions (indra_db.util.helpers)

Functions with broad utility throughout the repository, but otherwise miscellaneous.

Routines for Inserting Statements and Content (indra_db.util.insert)

Inserting content into the database can be a rather involved process, but here are defined high-level utilities to uniformly accomplish the task.