Using an external database with Spire

If your lab already has a database of reconstruction projects, Spire can communicate with it. This generally occurs at the beginning and end of a project. At the start of a project Spire can download some project parameters (e.g., electron voltage, pixel resolution, etc) from the database. At the end of a project, final volumes, resolution information, etc. can be uploaded into the database.

Since Spire does not know which database you are using, nor anything about the internal organization of that database, you will have to supply that information. This usually means
- installing an additional Python database library,
- writing some Python code that enables Spire to access your database (code for MySQL is included in Spire package).

Setting up Spire to connect to an external database:

  1. Find, install, and test the Python module for the database you are using.
    For MySQL, this means installing MySQLdb, which can be downloaded from For other databases, Python modules for connecting to Informix, Ingres, ODBC, Oracle, Postgres, Sybase and others are at They usually come with some python test programs - use the test programs to make sure Python can connect properly with your database.
  2. Create a module for Spire, called
    For MySQL, such a module is included in the Spire package, called This file should be copied to
    For other databases, write a similar Python module for your database, using as a template (see an example). This module must contain a class spiderDatabase, which inherits from spiderClasses.SpiderDatabase. This class object must have the following attributes and methods:

    databaseNamea database name to present to the user, e.g., "the Project Database"
    idthe project ID number is used to specify a particular project in the database.
    projectqueryanother SQL query to fetch project information
    __init__()sets the required attributes.
    isExtDatabaseAlive()returns 1 or 0 depending on whether it can successfully connect.
    sendQuery(query)returns results of SQL statement
    getProjectInfo()using projectquery, fetches project information, and inserts it into GB.P, the internal class object of the current Spire project.
    upload(upload_object)given an uploadable object, establish a connection and insert data into appropriate places in the external database

  3. Copy your database module to in $PYTHONPATH/site-packages/Spire

Example: setting up Spire to connect to a MySQL database

The Spire distribution contains example code for a tiny project database in MySQL.

You must first:

  • have MySQL installed,
  • have the MySQL server started,
  • have the Python mySQL interface, MySQLdb, installed
    (download from
  • create the test database with, which creates a table in the specified database and inserts some test data in it. Usage: -u user -p password -d database -t table

    All arguments are optional. If you type just

    it will use the following default values:
    database = "test_spire"
    table = "projects"
    user = "" i.e., anonymous login must be enabled for mysql
    password = "" will create the table projects in the database test_spire and put some values in the table.

    Data loaded into table 'projects':
    | project_id | pixelsize | kev  | project_file | data_ext |
    | 149        | 4.78      | 100  | proj149      | xyz      |
    "database", "user", and "password" must be set up for your MySQL database.
    "newtable" is the name of the new table created to hold project information. database user password table

    puts sample project data into the table.

    E.g., for database 'test' and user 'brian', whose password is 'heinz57' test brian heinz57 projects

    creates a new table called 'projects' (note this is not a secure way to handle passwords) test brian heinz57 projects

    then loads the test data.

    copy this file,, to, and run Spire. Start a new project, enter project number 149. It should fetch data from the MySQL database.