R/getPatientSet.R

In transmart/RInterface: R Client for accessing the tranSMART RESTful API

# Copyright 2014, 2015 The Hyve B.V.
#
# 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/>..

getPatientSet <- function(id) {
    if (!is.numeric(id) || id %% 1 != 0 || id < 0) {
        stop(paste(id, "is not a valid positive integer"))
    }
    .ensureTransmartConnection()

    patientSet <- .transmartGetJSON(paste0("/patient_sets/", id))

    # Don't expose id, it should not be used and will be removed from a future version of rest-api
    # COMPAT: remove this block if support for the old rest-api is dropped.
    if (length(patientSet$patients) && "id" %in% names(patientSet$patients[[1]])) {
        for (i in seq_along(patientSet$patients)) {
            patientSet$patients[[i]]$id <- NULL
        }
    }

    names(patientSet$patients) <- sapply(patientSet$patients, function(p) {p$inTrialId})
    patientSet
}