Merge branch 'master' into bugfixes

Author: JanKanis

R/getPatientSets.R R/getPatientSet.RR/getPatientSets.R renamed to R/getPatientSet.R

@@ -1,5 +1,4 @@
 # 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.
@@ -28,7 +27,7 @@ getPatientSet <- function(id) {
     }
     .ensureTransmartConnection()
 
-    patientSet <- .transmartGetJSON(paste("/patient_sets/", id, sep=''))
+    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.

R/getSubjects.R

@@ -31,6 +31,14 @@ getSubjects <- function(study.name, as.data.frame = TRUE) {
     subjectIDs <- sapply(listOfSubjects, FUN = function(x) { x$inTrialId })
     names(listOfSubjects) <- subjectIDs
 
+    # 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(listOfSubjects) && "id" %in% names(listOfSubjects[[1]])) {
+        for (i in seq_along(patientSet$patients)) {
+            listOfSubjects[[i]]$id <- NULL
+        }
+    }
+
     if (as.data.frame) return(.listToDataFrame(listOfSubjects))
     listOfSubjects
 }

man/transmartRClient-package.Rd

@@ -12,26 +12,18 @@ RESTful API. The R client currently allows a user to retrieve both clinical
 and high dimensional data (to which the user is authorized to access).
 }
 \details{
-  \tabular{ll}{
-    Package: \tab transmartRClient\cr
-    Type: \tab Package\cr
-    Version: \tab 0.2\cr
-    Date: \tab 2014-02-26\cr
-    License: \tab GPL-3 and higher \cr
-  }
-  
-  \cr
-  
-  The following functions are available in the package:
+
+The following functions are available in the package:
   \tabular{l}{
   \code{\link{connectToTransmart}}\cr
   \code{\link{getStudies}}\cr
   \code{\link{getSubjects}}\cr
   \code{\link{getConcepts}}\cr
   \code{\link{getObservations}}\cr
   \code{\link{getHighdimData}}\cr
+  \code{\link{highdimInfo}}\cr
+  \code{\link{getPatientSet}}\cr
   \code{\link{getPatientSetID}}\cr
-
 }
 }