LodestarConn: R6 Class for abstracting database connections and maintaining...

In sagrudd/gwangmyeongseong3: What the Package Does (One Line, Title Case)

Description

This class aims to provide some basic minimal functionality for interacting with a Lodestar schema in a relational database. A key ambition at outset has been the separation of user credentials and demonstration code for the preparation of examples and documentation in the vignettes.

Methods

Public methods

• LodestarConn$new()

• LodestarConn$connection()

• LodestarConn$as_list()

• LodestarConn$list_tables()

• LodestarConn$drop_table()

• LodestarConn$fastx_upload()

• LodestarConn$clone()

---

Method new()

Creates a new LodestarConn object. This initialisation method orchestrates other sanity checking of the defined parameters(s) to ensure that the environment is coherent and tractable

Usage

LodestarConn$new(
  backend = NA,
  keyring = .default_keyring,
  service = .default_service,
  username = NA,
  password = NA,
  port = 5432,
  silent = FALSE
)

Arguments

backend

keyring backend object used to define username and password independently of the vignette code (persistence) - NA by default

• software will endeavour to select backend on basis of available keyring context

keyring

which of the available keyrings will hold the connection details - lodestar by default.

service

the name of the database that we'll endeavour to connect to - this will be parsed from the backend context - lodestar by default.

username

the user account to be used with the database - NA by default; in simpler installations the software will identify the username on basis of e.g. service

password

the password to connect to the database with; using the backend object this can be read from the keyring

silent

boolean defining whether logging of process should be performed (TRUE by default)

Returns

the LodestarConn R6 object

---

Method connection()

Get a database connection corresponding to the passed parameters

Usage

LodestarConn$connection()

Returns

a DBI connection object

---

Method as_list()

export the key characteristics of this object in a format for writing to YAML to allow the propagation of settings in a cluster environment where we cannot expect processes to have access to the keyring - this does mean that connection strings and passwords are written to file ... this will be addressed more securely once we're beyond the proof-of- concept.

Usage

LodestarConn$as_list()

---

Method list_tables()

Usage

LodestarConn$list_tables(schema = "public")

---

Method drop_table()

Usage

LodestarConn$drop_table(table)

---

Method fastx_upload()

Usage

LodestarConn$fastx_upload(dna, table = "cluster_fasta", fastx = "fasta")

---

Method clone()

The objects of this class are cloneable with this method.

Usage

LodestarConn$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

sagrudd/gwangmyeongseong3 documentation built on Jan. 25, 2021, 5:44 a.m.