Making some changes to the latest version.

Removing legacy/harmonized from folder structure

Fixing #573
Fixing #574

Needs more checking with CNV and CPTAC-3 projects

NAMESPACE

@@ -109,6 +109,7 @@ importFrom(dplyr,mutate_all)
 importFrom(dplyr,pull)
 importFrom(dplyr,row_number)
 importFrom(dplyr,slice)
+importFrom(dplyr,summarise)
 importFrom(grDevices,dev.list)
 importFrom(grDevices,dev.off)
 importFrom(grDevices,pdf)

NEWS

@@ -2,6 +2,7 @@ CHANGES IN VERSION 2.29.1
 -------------------------
 
 * Removing support to legacy archive since it will be shutdown by GDC soon.
+* When saving files we will not include folders prefix  legacy/harmonized anymore
 
 CHANGES IN VERSION 2.21.1
 -------------------------

R/clinical.R

@@ -170,6 +170,7 @@ TCGAquery_MatchedCoupledSampleTypes <- function(barcode,typesample){
 #' @export
 #' @importFrom data.table rbindlist as.data.table
 #' @importFrom jsonlite fromJSON
+#' @importFrom dplyr summarise
 #' @examples
 #' clinical <- GDCquery_clinic(
 #'    project = "TCGA-ACC",
@@ -348,7 +349,10 @@ GDCquery_clinic <- function(
                                 # we will collapse them into one single row
                                 # concatanating all columns using ;
                                 aux <- x %>% dplyr::group_by(submitter_id) %>%
-                                    summarise(across(everything(),~ paste(unique(.), collapse = ";")))
+                                    dplyr::summarise(
+                                        across(everything(),~ paste(unique(.), collapse = ";"))
+                                    )
+
                                 aux$treatments <- list(dplyr::bind_rows(x$treatments))
                                 aux
                             }
@@ -440,7 +444,7 @@ GDCquery_clinic <- function(
 #' query <- GDCquery(
 #'   project = "TCGA-COAD",
 #'   data.category = "Clinical",
-#'   file.type = "xml",
+#'   data.format = "bcr xml",
 #'   barcode = c("TCGA-RU-A8FL","TCGA-AA-3972")
 #' )
 #' GDCdownload(query)
@@ -452,7 +456,7 @@ GDCquery_clinic <- function(
 #' query <- GDCquery(
 #'    project = "TCGA-COAD",
 #'    data.category = "Biospecimen",
-#'    file.type = "xml",
+#'    data.format = "bcr xml",
 #'    data.type = "Biospecimen Supplement",
 #'    barcode = c("TCGA-RU-A8FL","TCGA-AA-3972")
 #' )
@@ -503,9 +507,9 @@ GDCprepare_clinic <- function(
     }
 
     # Get all the clincal xml files
-    source <- "harmonized"
+
     files <- file.path(
-        query$results[[1]]$project, source,
+        query$results[[1]]$project,
         gsub(" ","_",query$results[[1]]$data_category),
         gsub(" ","_",query$results[[1]]$data_type),
         gsub(" ","_",query$results[[1]]$file_id),
@@ -586,16 +590,18 @@ GDCprepare_clinic <- function(
         message("Updating days_to_last_followup and vital_status from follow_up information using last entry")
         followup <- parseFollowup(files,xpath,clinical.info)
 
-        followup_last <- followup %>% dplyr::group_by(bcr_patient_barcode) %>% dplyr::summarise(
-            days_to_last_followup = max(as.numeric(days_to_last_followup),na.rm = TRUE),
-            vital_status = vital_status[
-                ifelse(
-                    any(followup$days_to_last_followup %in% ""),
-                    which(followup$days_to_last_followup %in% ""),
-                    which.max(days_to_last_followup)
-                )
-            ]
-        )
+        followup_last <- followup %>%
+            dplyr::group_by(bcr_patient_barcode) %>%
+            dplyr::summarise(
+                days_to_last_followup = max(as.numeric(days_to_last_followup),na.rm = TRUE),
+                vital_status = vital_status[
+                    ifelse(
+                        any(followup$days_to_last_followup %in% ""),
+                        which(followup$days_to_last_followup %in% ""),
+                        which.max(days_to_last_followup)
+                    )
+                ]
+            )
         clin$days_to_last_followup <- followup_last$days_to_last_followup[match(clin$bcr_patient_barcode,followup_last$bcr_patient_barcode)]
         clin$vital_status <- followup_last$vital_status[match(clin$bcr_patient_barcode,followup_last$bcr_patient_barcode)]
     }

R/download.R

@@ -64,8 +64,6 @@ GDCdownload <- function(
         stop("We can only download one data type. Please use data.type argument in GDCquery to filter results.")
     }
 
-    source <- "harmonized"
-
     dir.create(directory, showWarnings = FALSE, recursive = TRUE)
     for(proj in unique(unlist(query$project))){
         message("Downloading data for project ", proj)
@@ -77,7 +75,7 @@ GDCdownload <- function(
 
         path <- unique(
             file.path(
-                proj, source,
+                proj,
                 gsub(" ","_", results$data_category),
                 gsub(" ","_",results$data_type))
         )