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title: Database connection topic: About data curation order: 2 ...

The ISDB tools expect to connect to a PostgreSQL (Pg) database for storing and retrieving data. The Pg database software may be running on the local computer or on a remote server.

All of the ISDB tools are designed to use connection details controlled by standard PostgreSQL environment variables and configuration files. This document describes how to specify those connection details and the assumptions the ISDB tools make.

Specifying connection details

The database name should be specified by PGDATABASE. The ISDB tools default the database name to isdb if unspecified. You may only have occasion to change this if accessing frozen versions of the ISDB.

The location of the Pg server should be specified by PGHOST. If you're working with a Pg database on the same machine as the ISDB tools, you can usually leave PGHOST unset.

The Pg user should be specified by setting PGUSER. If left unset, Pg uses the username of the person running the command.

Passwords should be specified in a password file rather than interactively or on the command line. Your Pg server may also use GSS-API or Kerberos authentication in which case you'd rely on your normal mechanisms for authenticating.

You may also use a service file definition containing host and user by setting PGSERVICE. The ISDB tools forcibly default the database name to isdb if PGDATABASE isn't set, however, so any database named in the service definition will effectively be ignored. (This may be remedied in the future, as service definitions are handy!)

Example

Below is an example of how to specify database connection details on the command line when running an ISDB tool:

env PGUSER=isdb_rw PGHOST=ireland ~/isdb/bin/load-source --reload sources/Wagner-2014-Science/

This tells the tool to connect to a computer named ireland as the user named isdb_rw. The database name is unspecified, so it defaults to isdb.

The load-source tool is responsible for all aspects of taking an ISDB data source and loading it into the database. However, the particulars of specifying database connection details are the same across all ISDB tools.