feat: add upload in long format

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dsUpload
 Title: Upload Functions for DataSHIELD Backends
-Version: 4.4.4.9000
+Version: 4.5.0
 Authors@R: 
   c(person(given = "Sido",
       family = "Haakma",

R/enums.R

@@ -38,6 +38,13 @@ du.enum.dict.kind <- function() {
   list(CORE = "core", OUTCOME = "outcome", BETA = "beta")
 }
 
+#' Source data types
+#'
+#' @noRd
+du.enum.data.type <- function() {
+  list(LONG = "long", WIDE = "wide")
+}
+
 #' Projects that are containing dictionaries. Repositories containing these dictionaries should be:
 #'
 #' - ds-dictionaries

R/reshape.R

@@ -2,18 +2,20 @@
 #'
 #' @param upload do you want automatically upload the files to your opal (default = true)
 #' @param data_version version of the data you are going to upload into Opal
+#' @param data_type default = WIDE, can be LONG as well
 #' @param input_format possible formats are CSV,STATA,SPSS or SAS (default = CSV)
 #' @param dict_version version of the dictionary
 #' @param dict_kind kind of data to reshape (default = core)
 #' @param input_path path for import file
 #' @param run_mode default = NORMAL, can be TEST and NON_INTERACTIIVE
+
 #'
 #' @importFrom readxl read_xlsx
 #'
 #' @noRd
-du.reshape <- function(upload = TRUE, project, data_version, input_format, dict_version, dict_kind, input_path, run_mode) {
+du.reshape <- function(upload = TRUE, project, data_version, data_type, input_format, dict_version, dict_kind, input_path, run_mode) {
   message("######################################################")
-  message("  Start converting and uploading data                 ")
+  message(paste0("  Start converting and uploading data  ( ", data_type, "-format )"))
   message("######################################################")
   message("* Setup: load data and set output directory")
   message("------------------------------------------------------")
@@ -28,24 +30,50 @@ du.reshape <- function(upload = TRUE, project, data_version, input_format, dict_
   file_name_monthly <- paste0(file_prefix, "_", data_version, "_", "monthly_repeated_measures")
   file_name_yearly <- paste0(file_prefix, "_", data_version, "_", "yearly_repeated_measures")
 
-  nonrep_data <- du.reshape.generate.non.repeated(
-    data, dict_kind
-  )
+  if(data_type == du.enum.data.type()$WIDE) {
+    nonrep_data <- du.reshape.wide.generate.non.repeated(
+      data, dict_kind
+    )
+  } else {
+    nonrep_data <- du.reshape.long.generate.non.repeated(
+      data, dict_kind
+    )
+  }
   if (!is.null(nonrep_data)) write_csv(nonrep_data, paste0(getwd(), "/", file_name_nonrep, ".csv"), na = "")
-  yearlyrep_data <- du.reshape.generate.yearly.repeated(
-    data, dict_kind
-  )
+
+  if(data_type == du.enum.data.type()$WIDE) {
+    yearlyrep_data <- du.reshape.wide.generate.yearly.repeated(
+      data, dict_kind
+    )
+  } else {
+    #yearlyrep_data <- du.reshape.long.generate.yearly.repeated(
+    #  data, dict_kind
+    #)
+  }
   if (!is.null(yearlyrep_data)) write_csv(yearlyrep_data, paste0(getwd(), "/", file_name_yearly, ".csv"), na = "")
-  monthlyrep_data <- du.reshape.generate.monthly.repeated(
-    data, dict_kind
-  )
+
+  if(data_type == du.enum.data.type()$WIDE) {
+    monthlyrep_data <- du.reshape.wide.generate.monthly.repeated(
+      data, dict_kind
+    )
+  } else {
+    #monthlyrep_data <- du.reshape.long.generate.monthly.repeated(
+    #  data, dict_kind
+    #)
+  }
   if (!is.null(monthlyrep_data)) write_csv(monthlyrep_data, paste0(getwd(), "/", file_name_monthly, ".csv"), na = "")
 
   if (dict_kind == du.enum.dict.kind()$OUTCOME) {
     file_name_weekly <- paste0(file_prefix, "_", data_version, "_", "weekly_repeated_measures")
-    weeklyrep_data <- du.reshape.generate.weekly.repeated(
-      data, dict_kind
-    )
+    if(data_type == du.enum.data.type()$WIDE) {
+      weeklyrep_data <- du.reshape.wide.generate.weekly.repeated(
+        data, dict_kind
+      )
+    } else {
+      #weeklyrep_data <- du.reshape.long.generate.weekly.repeated(
+      #  data, dict_kind
+      #)
+    }
     if (!is.null(weeklyrep_data)) {
       write_csv(weeklyrep_data, paste0(getwd(), "/", file_name_weekly, ".csv"), na = "")
       weeklyrep_metadata <- du.retrieve.full.dict(du.enum.table.types()$WEEKLY, dict_kind)
@@ -63,9 +91,15 @@ du.reshape <- function(upload = TRUE, project, data_version, input_format, dict_
 
   if (dict_kind == du.enum.dict.kind()$CORE & dict_version != "1_0") {
     file_name_trimester <- paste0(file_prefix, "_", data_version, "_", "trimester_repeated_measures")
-    trimester_data <- du.reshape.generate.trimesterly.repeated(
-      data, dict_kind
-    )
+    if(data_type == du.enum.data.type()$WIDE) {
+      trimester_data <- du.reshape.wide.generate.trimesterly.repeated(
+        data, dict_kind
+      )
+    } else {
+      #trimester_data <- du.reshape.long.generate.trimesterly.repeated(
+      #  data, dict_kind
+      #)
+    }
     if (!is.null(trimester_data)) {
       write_csv(trimester_data, paste0(getwd(), "/", file_name_trimester, ".csv"), na = "")
       trimester_metadata <- du.retrieve.full.dict(du.enum.table.types()$TRIMESTER, dict_kind)

R/reshape_helpers.R → R/reshape_long.R

@@ -157,7 +157,7 @@ du.check.nas <- function(stripped, raw) {
 #' @importFrom readxl read_xlsx
 #'
 #' @noRd
-du.reshape.generate.non.repeated <- function(data, dict_kind) {
+du.reshape.long.generate.non.repeated <- function(data, dict_kind) {
   message("* Generating: non-repeated measures")
 
   # Retrieve dictionary
@@ -193,7 +193,7 @@ du.reshape.generate.non.repeated <- function(data, dict_kind) {
 #' @importFrom tidyr gather
 #'
 #' @noRd
-du.reshape.generate.yearly.repeated <- function(data, dict_kind) {
+du.reshape.long.generate.yearly.repeated <- function(data, dict_kind) {
   # workaround to avoid glpobal variable warnings, check:
   # https://stackoverflow.com/questions/9439256/how-can-i-handle-r-cmd-check-no-visible-binding-for-global-variable-notes-when
   orig_var <- value <- age_years <- . <- NULL
@@ -265,7 +265,7 @@ du.reshape.generate.yearly.repeated <- function(data, dict_kind) {
 #' @importFrom tidyr gather
 #'
 #' @noRd
-du.reshape.generate.monthly.repeated <- function(data, dict_kind) {
+du.reshape.long.generate.monthly.repeated <- function(data, dict_kind) {
   # workaround to avoid glpobal variable warnings, check:
   # https://stackoverflow.com/questions/9439256/how-can-i-handle-r-cmd-check-no-visible-binding-for-global-variable-notes-when
   orig_var <- value <- age_months <- . <- NULL
@@ -339,7 +339,7 @@ du.reshape.generate.monthly.repeated <- function(data, dict_kind) {
 #' @importFrom tidyr gather
 #'
 #' @noRd
-du.reshape.generate.weekly.repeated <- function(data, dict_kind) {
+du.reshape.long.generate.weekly.repeated <- function(data, dict_kind) {
   # workaround to avoid glpobal variable warnings, check:
   # https://stackoverflow.com/questions/9439256/how-can-i-handle-r-cmd-check-no-visible-binding-for-global-variable-notes-when
   orig_var <- value <- age_weeks <- . <- NULL # Gestational age in weeks
@@ -415,7 +415,7 @@ du.reshape.generate.weekly.repeated <- function(data, dict_kind) {
 #' @importFrom tidyr gather
 #'
 #' @noRd
-du.reshape.generate.trimesterly.repeated <- function(data, dict_kind) {
+du.reshape.long.generate.trimesterly.repeated <- function(data, dict_kind) {
   # workaround to avoid glpobal variable warnings, check:
   # https://stackoverflow.com/questions/9439256/how-can-i-handle-r-cmd-check-no-visible-binding-for-global-variable-notes-when
   orig_var <- value <- age_trimester <- . <- NULL