# Copyright 2014, 2015 The Hyve B.V.
# 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) {
.ensureTransmartConnection()
serverResult <- .transmartGetJSON(paste("/studies/", study.name, "/concepts", sep = ""))
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
}
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