Opal stores data and meta-data in projects that are accessible through web services. See the Variables and Data documentation page that explains the data model of Opal. The Opal R package exposes projects related functions:
Note that these functions do not create a R session on the server side: it is only accessing the content of the Opal server (permission checks apply).
Setup the connection with Opal:
library(opalr)
o <- opal.login("administrator", "password", "https://opal-demo.obiba.org")List the projects:
opal.projects(o)List the datasources (there is one per project) to get the details about how the data are persisted and what are the tables:
opal.datasources(o)List the tables in a datasource, with their count of variables and entities:
opal.tables(o, datasource = "CPTP", counts = TRUE)List the variables of a table and get the details of the variable annotations (one column per variable attribute with namespace):
opal.variables(o, datasource = "CPTP", table = "Coreqx_final")Get the values in a table for a specific entity:
opal.valueset(o, datasource = "FNAC", table = "FNAC", identifier = "1000502517535681229")Variable attributes can be described by taxonomies. List the taxonomies:
opal.taxonomies(o)List the vocabularies of a taxonomy:
opal.vocabularies(o, taxonomy = "Mlstr_area")List the terms of a vocabulary:
opal.terms(o, taxonomy = "Mlstr_area", vocabulary = "Lifestyle_behaviours")Good practice is to free server resources by sending a logout request:
opal.logout(o)