R/getConcepts.R

In thehyve/heim-RInterface: R Client for accessing the tranSMART RESTful API

# Copyright 2014 Janssen Research & Development, LLC.
#
# This file is part of tranSMART R Client: R package allowing access to
# tranSMART's data via its RESTful API.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation, either version 3 of the License, or (at your
# option) any later version, along with the following terms:
#
#   1. You may convey a work based on this program in accordance with
#      section 5, provided that you retain the above notices.
#   2. You may convey verbatim copies of this program code as you receive
#      it, in any medium, provided that you retain the above notices.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program. If not, see <http://www.gnu.org/licenses/>.

getConcepts <- function(study.name, as.data.frame = TRUE, cull.columns = TRUE) {
    .checkTransmartConnection()
    
    serverResult <- .transmartServerGetRequest(
            paste("/studies/", study.name, "/concepts", sep = ""), accept.type = "hal")
    listOfConcepts <- serverResult$ontology_terms
    
    if (as.data.frame) {
        dataFrameConcepts <- .listToDataFrame(listOfConcepts)
        if (cull.columns) {
            columnsToCull <- match(c("key"), names(dataFrameConcepts))
            if (any(is.na(columnsToCull))) {
                warning("There was a problem culling columns. You can try again with cull.columns = FALSE.")
                message("Sorry. You've encountered a bug.\n",
                        "You can help fix it by contacting us. Type ?transmartRClient for contact details.\n",
                        "Optional: type options(verbose = TRUE) and replicate the bug to find out more details.")
            }
            return(dataFrameConcepts[, -columnsToCull])
        }
        return(dataFrameConcepts)
    }
    
    listOfConcepts
}