Using an access token

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Setting your token

As of today, two databases require an access token: ChemSpider and Peakforest.

There are four ways to set an access token in biodb:

• Through environment variables.
• Through the BiodbConfig class instance.
• When creating explicitly a connector instance.
• Directly on the database information class (BiodbDbInfo) instance.

The environment variables and biodb configuration keys you must use to set your access tokens are:

Database	biodb configuration key	Environment variable
PeakForest Mass	peakforest.mass.token	BIODB_PEAKFOREST_MASS_TOKEN
PeakForest Compound	peakforest.compound.token	BIODB_PEAKFOREST_COMPOUND_TOKEN
ChemSpider	chemspider.token	BIODB_CHEMSPIDER_TOKEN

To set your ChemSpider access token using the environment variables under UNIX/Linux systems:

export BIODB_CHEMSPIDER_TOKEN=01234567-89ab-cdef-0123-456789abcdef

The environment variable is used by the BiodbConfig class instance if available. However you can also use the BiodbConfig class instance directly:

mybiodb <- biodb::Biodb$new()
mybiodb$getConfig()$set('chemspider.token', '01234567-89ab-cdef-0123-456789abcdef')

To set the token directly on the DbInfo instance:

mybiodb <- biodb::Biodb$new()
dbsinfo <- mybiodb$getDbsInfo()
dbsinfo$get('chemspider')$setToken('01234567-89ab-cdef-0123-456789abcdef')

To set the token when instantiating the connector with the factory:

mybiodb <- biodb::Biodb$new()
factory <- mybiodb$getFactory()
conn <- factory$createConn('chemspider', token = '01234567-89ab-cdef-0123-456789abcdef')

Accessing the database

You should then be able to access the database normally.