In pkrog/biodb: biodb, a library and a development framework for connecting to chemical and biological databases

Purpose

{{pkgName}} is a biodb extension package that implements a connector to {{dbTitle}}.

Initialization

The first step in using {{pkgName}}, is to create an instance of the biodb class Biodb from the main biodb package. This is done by calling the constructor of the class:

mybiodb <- biodb::newInst()

During this step the configuration is set up, the cache system is initialized and extension packages are loaded.

We will see at the end of this vignette that the biodb instance needs to be terminated with a call to the terminate() method.

Creating a connector to {{dbTitle}}

In biodb the connection to a database is handled by a connector instance that you can get from the factory. {{pkgName}} implements a connector to a remote database. Here is the code to instantiate a connector:

conn <- mybiodb$getFactory()$createConn('{{dbName}}')

{{pkgName}} implements a connector to a local database, thus when creating an instance you must provide a URL that points to your database:

conn <- mybiodb$getFactory()$createConn('{{dbName}}', url=file.path('path', 'to', 'my', 'db.file))

Accessing entries

To get the number of entries stored inside the database, run:

conn$getNbEntries()

To get some of the first entry IDs (accession numbers) from the database, run:

ids <- conn$getEntryIds(2)
ids

To retrieve entries, use:

entries <- conn$getEntry(ids)
entries

To convert a list of entries into a dataframe, run:

x <- mybiodb$entriesToDataframe(entries)
x

Running the "find" web service

You can access the web service "find" directly with the wsFind method:

conn$wsFind(name="abc", retfmt="ids")

Closing biodb instance

When done with your biodb instance you have to terminate it, in order to ensure release of resources (file handles, database connection, etc):

mybiodb$terminate()

pkrog/biodb documentation built on Nov. 29, 2022, 4:24 a.m.