Database

Overview

The framework provides capabilities to interact with an sqlite database, in order to store objects such as PointIsotherm, ModelIsotherm, Adsorbate, Material.

The database was initially envisioned as a centralised data storage for the MADIREL Laboratory in Marseille. To generalize the concept for this framework, the database has been simplified to what the authors consider bare bones, but still extensible, functionality. Suggests for further improvements are welcome.

Note

For most purposes, the internal database is adequate for storage and retrieval. However, it can be difficult to locate it on the disk, and, depending on the amount of data it stores, it can grow to a considerable size. Consider using a separate database file.

Database structure

A diagram of the database schema can be seen below:

The database is configured to use foreign keys, in order to prevent data redundancy and to enforce error checking. This will make sure that no stored isotherm has an unknown or misspelled adsorbate but it also means that some groundwork is required before uploading the first isotherm.

Database methods

All the functions which interact with a database take the database path as their first argument. If the internal database is to be used, the parameter passed should be the pygaps.DATABASE reference. A complete list of methods can be found in the sqlite reference.

Database example

Check out the Jupyter notebook in the examples section

Blank database creation

The internal database is already created and usable when pyGAPS is installed. If the user decides to have an external database, they can either copy the internal database (located in the pygaps/database directory) or generate an empty one using the db_create command.

from pygaps.utilities.sqlite_db_creator import db_create
db_create("path/to/database")