Initializing biodb

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Introduction

First of all, before using biodb, you need to create an instance of the main class Biodb. This is done by calling the constructor of the class through the new() method. The OOP (Object Oriented Programming) system used in the biodb package is the R5 system also called Reference Classes. In this system, the created objects are not copied, but their reference are copied. This means than when you pass an instance to a function, that function is able to modify the instance.

To create an instance of the Biodb class, call the constructor method:

mybiodb <- biodb::Biodb()

This is will create a Biodb instance and put its reference into the mybiodb variable. Calling new() without any argument configures the instance with the default values.

Observers

By default, the Biodb instance will be configured with a console logger (instance of the class BiodbLogger), which will print all biodb messages to the console. You can disable this default logger by setting the logger argument to false:

mybiodb <- biodb::Biodb$new(logger = FALSE)

In this case, only the normal R warnings and errors will be printed.

Setting your own instance of the BiodbLogger class

You can also set your own instance of BiodbLogger, using the observers argument, in order for instance to redirect the output to a file:

mybiodb <- biodb::Biodb$new(logger = FALSE, observers = biodb::BiodbLogger$new(file = 'mybiodb.log'))

If you want both have the logger output written to the console and into a file, just define two instances of the BiodbLogger class:

mybiodb <- biodb::Biodb$new(logger = FALSE, observers = list(biodb::BiodbLogger$new(), biodb::BiodbLogger$new(file = 'mybiodb2.log')))

See the documentation of the BiodbLogger class for more details.

Defining your own observers

If you wish, you can also define your own observers that inherit from the BiodbObserver class, and set them through the observers argument.

Setting observers after the instance has been created

It is also possible to add an observer during the life of your biodb instance:

mybiodb$addObservers( list(biodb::BiodbLogger$new(), biodb::BiodbLogger$new(file = 'mybiodb3.log')))

Getting a list of current observers

Here is how to obtain a list of all observers currently defined:

mybiodb$getObservers()

The singleton classes

Several singleton classes are defined in biodb. Their instances are all accessible from the Biodb instance you've created.

To get the factory instance:

factory <- mybiodb$getFactory()

To get the configuration instance:

config <- mybiodb$getConfig()

To get the cache system instance:

cache <- mybiodb$getCache()

To get the database information instance:

dbsinfo <- mybiodb$getDbsInfo()

To get the entry fields instance:

entry.fields <- mybiodb$getEntryFields()