connectToBed: Connect to a neo4j BED database

In patzaw/BED: Biological Entity Dictionary (BED)

Connect to a neo4j BED database

Description

Connect to a neo4j BED database

Usage

connectToBed(
  url = NULL,
  username = NULL,
  password = NULL,
  connection = 1,
  remember = FALSE,
  useCache = NA,
  importPath = NULL,
  .opts = list()
)

Arguments

url	a character string. The host and the port are sufficient (e.g: "localhost:5454")
username	a character string
password	a character string
connection	the id of the connection already registered to use. By default the first registered connection is used.
remember	if TRUE connection information is saved localy in a file and used to automatically connect the next time. The default is set to FALSE. All the connections that have been saved can be listed with lsBedConnections and any of them can be forgotten with forgetBedConnection.
useCache	if TRUE the results of large queries can be saved locally in a file. The default is FALSE for policy reasons. But it is recommended to set it to TRUE to improve the speed of recurrent queries. If NA (default parameter) the value is taken from former connection if it exists or it is set to FALSE.
importPath	the path to the import folder for loading information in BED (used only when feeding the database ==> default: NULL)
.opts	a named list identifying the curl options for the handle (see neo2R::startGraph()).

Details

Be careful that you should reconnect to BED database each time the environment is reloaded. It is done automatically if remember is set to TRUE.

Information about how to get an instance of the BED 'Neo4j' database is provided here:

• https://github.com/patzaw/BED#bed-database-instance-available-as-a-docker-image

• https://github.com/patzaw/BED#build-a-bed-database-instance

Value

This function does not return any value. It prepares the BED environment to allow transparent DB calls.

See Also

checkBedConn, lsBedConnections, forgetBedConnection

patzaw/BED documentation built on April 14, 2024, 10:46 p.m.