ndex_connect: Connect to NDEx REST API

In frankkramer-lab/ndexr: NDEx R client library

Connect to NDEx REST API

Description

This function creates an NDExConnection which stores options and authentication details. It is a parameter required for most of the other ndexr functions. If username and password are missing an anonymous connection is created, which already offers most of the retrieval functionality.

Usage

ndex_connect(
  username,
  password,
  host = ndexConf$connection$host,
  apiPath = ndexConf$connection$api,
  ndexConf = ndex_config,
  verbose = FALSE
)

Arguments

username	character (optional); username
password	character (optional); password
host	character (default: ndexConf$connection$host); Host address of NDEx server; By default the url set in ndexConf$defaults$connection$host is used. ("http://www.ndexbio.org")
apiPath	character (default: ndexConf$connection$api); URL path of the REST api; By default the url set in ndexConf$defaults$connection$api is used. ("/v2" for NDEx version 2.0, "/rest" for NDEx version 1.3)
ndexConf	config object (nested list, default: ndex_config); Configuration of NDEx REST server; Set in ndex_config (set in ndex_api_config.r or ndex_api_config.yml): It contains specifications for NDEx server api version 1.3 and 2.0. The default api is specified by 'defaultVersion'
verbose	logical (optional); whether to print out extended feedback

Value

returns object of class NDExConnection which stores options, authentication and api configuration if successfull, NULL otherwise

See Also

ndex_config

Examples

## log in anonymously
ndexcon = ndex_connect()
## same as above with extended feedback
ndexcon = ndex_connect(verbose=TRUE)
## Not run: 
## log in with credentials
ndexcon = ndex_connect('user','password')
## running some NDEx server locally
ndexcon = ndex_connect(host='localhost:8765')
## manually change the api and connection configuration
ndexcon = ndex_connect(ndexConf=ndex_config$Version_2.0)   

## End(Not run)

frankkramer-lab/ndexr documentation built on April 4, 2023, 7:19 p.m.