Additional functions

In addition to the Sequence and Collection classes and their methods, some more functions are available as part of the API:

Setting the verbosity

Most methods of the MetagenomeDB API log messages about the information they process, the result of this processing, and their interaction with the underlying database. Those messages are of three different types, listed here from the least to the most important (or severe):

• debug messages: debugging messages as encountered during code execution. Those are useful only to keep track of low-level processes, such as object addition or query. Except for debugging purpose those messages are not important for the normal use of the API, and are filtered out by default.
• warning messages: reports conditions that might cause a problem in the future but are not immediately preventing the normal execution of your code. Typically, this is when the API falls back on default behavior after an invalid request is made (e.g., access to an non-existent database, or deletion of an uncommitted object). The user should be aware of this default behavior and act accordingly, as it may change the behavior of his code in way he didn’t expect. By default, all messages of this level and above are displayed.
• error messages: reports conditions that typically prevent the normal execution of your code. You must address the issue and re-execute the failed instruction(s).

The following functions allow to filter the type of messages that will be displayed on the standard error stream when using the API:

MetagenomeDB.max_verbosity()

Set the verbosity to the maximal level.

Note

Equivalent to set_verbosity() with level set to “debug”

MetagenomeDB.min_verbosity()

Set the verbosity to the minimal level.

Note

Equivalent to set_verbosity() with level set to “error”

MetagenomeDB.normal_verbosity()

Set the verbosity to the normal level.

Note

Equivalent to set_verbosity() with level set to “warning”

MetagenomeDB.set_verbosity(level)

Set the verbosity level for the MetagenomeDB API.

Parameters:

• level: either ‘debug’, ‘warning’ or ‘error’ (case insensitive). Only messages of this level or above will be displayed.

Example of use:

>>> import MetagenomeDB as mdb
>>> mdb.max_verbosity()
2010-11-22 15:08:06,873 DEBUG: Verbosity set to 'debug'. set_verbosity() in __init__.py, line 34

Similarly, all command-line tools have a -v (or --verbose) option to set verbosity to its maximum.

Connecting to the database

By default, information about how the toolkit must connect to the MongoDB server are stored in a file .MetagenomeDB in the home directory (see Installation). However you can override those settings by using the connect() method:

MetagenomeDB.connection.connect(host='localhost', port=27017, database='MetagenomeDB', user='', password='')

Override server connection information.

Parameters:

• host: host of the MongoDB server (optional). Default: ‘localhost’
• port: port of the MongoDB server (optional). Default: 27017
• database: database within the MongoDB server (optional). Default: ‘MetagenomeDB’
• user: user for a secured MongoDB connection (optional)
• password: password for a secured MongoDB connection (optional)

Note

If connect() is not called, the connection information are read in the ‘~/.MetagenomeDB’ file.