Merge pull request #110 from lifecycle-project/fix/missing-yearly-mon…

…thly_4.6.0

Fix/missing yearly monthly 4.6.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dsUpload
 Title: Upload Functions for DataSHIELD Backends
-Version: 4.6.0
+Version: 4.6.1
 Authors@R: 
   c(person(given = "Mariska",
       family = "Slofstra",

R/reshape.R

@@ -32,19 +32,19 @@ du.reshape <- function(upload = TRUE, project, data_version, input_format, dict_
   nonrep_data <- du.reshape.generate.non.repeated(
     data, dict_kind
   )
-  if (exists("nonrep_data")) {
+  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 (exists("yearlyrep_data")) {
+  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 (exists('monthlyrep_data')) {
+  if (!is.null(monthlyrep_data)) {
     write_csv(monthlyrep_data, paste0(getwd(), "/", file_name_monthly, ".csv"), na = "")
   }
 
@@ -53,7 +53,7 @@ du.reshape <- function(upload = TRUE, project, data_version, input_format, dict_
     weeklyrep_data <- du.reshape.generate.weekly.repeated(
       data, dict_kind
     )
-    if (exists("weeklyrep_data")) {
+    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()$WEEKLY, dict_kind)
       weeklyrep_data <- du.add.metadata(weeklyrep_data, weeklyrep_metadata)
@@ -75,7 +75,7 @@ du.reshape <- function(upload = TRUE, project, data_version, input_format, dict_
     trimester_data <- du.reshape.generate.trimesterly.repeated(
       data, dict_kind
     )
-    if (exists("trimester_data")) {
+    if (!is.null(trimester_data)) {
       write_csv(trimester_data, paste0(getwd(), "/", file_name_trimester, ".csv"), na = "")
       trimester_metadata <- du.retrieve.full.dict(du.enum.table.types()$TRIMESTER, dict_kind)
       trimester_data <- du.add.metadata(trimester_data, trimester_metadata)
@@ -94,9 +94,9 @@ du.reshape <- function(upload = TRUE, project, data_version, input_format, dict_
 
   if (upload) {
     if (ds_upload.globals$login_data$driver == du.enum.backends()$OPAL) {
-      if (exists("nonrep_data")) du.opal.upload(dict_kind, file_name_nonrep)
-      if (exists("yearlyrep_data")) du.opal.upload(dict_kind, file_name_yearly)
-      if (exists("monthlyrep_data")){ du.opal.upload(dict_kind, file_name_monthly) }
+      if (!is.null(nonrep_data)) du.opal.upload(dict_kind, file_name_nonrep)
+      if (!is.null(yearlyrep_data)) du.opal.upload(dict_kind, file_name_yearly)
+      if (!is.null(monthlyrep_data)){ du.opal.upload(dict_kind, file_name_monthly) }
     }
     if (ds_upload.globals$login_data$driver == du.enum.backends()$ARMADILLO) {
       if (!is.null(nonrep_data)) { 

R/reshape_helpers.R

@@ -46,13 +46,17 @@ du.read.source.file <- function(input_path, input_format) {
 #'
 #' @noRd
 du.data.frame.remove.all.na.rows <- function(dataframe) {
-  df <- dataframe[-c(1)]
+  if(ncol(dataframe) >= 1) {
+    df <- dataframe[-c(1)]
 
-  naLines <- df %>%
-    is.na() %>%
-    apply(MARGIN = 1, FUN = all)
+    naLines <- df %>%
+      is.na() %>%
+      apply(MARGIN = 1, FUN = all)
 
-  return(df[!naLines, ])
+    return(df[!naLines, ])
+  } else {
+    return(list(0,0))
+  }
 }
 #'
 #' Matched the columns in the source data.
@@ -204,7 +208,7 @@ du.reshape.generate.yearly.repeated <- function(data, dict_kind) {
   matched_columns <- du.match.columns(colnames(data), variables_yearly_repeated_dict$name)
   yearly_repeated_measures <- data[matched_columns]
 
-  if (nrow(du.data.frame.remove.all.na.rows(yearly_repeated_measures)) <= 0) {
+  if (ncol(yearly_repeated_measures) <= 0 || nrow(du.data.frame.remove.all.na.rows(yearly_repeated_measures)) <= 0) {
     message("[WARNING] No yearly-repeated measures found in this set")
     return()
   }
@@ -276,7 +280,7 @@ du.reshape.generate.monthly.repeated <- function(data, dict_kind) {
   matched_columns <- du.match.columns(colnames(data), variables_monthly_repeated_dict$name)
   monthly_repeated_measures <- data[, matched_columns]
 
-  if (nrow(du.data.frame.remove.all.na.rows(monthly_repeated_measures)) <= 0) {
+  if (ncol(monthly_repeated_measures) <= 0 || nrow(du.data.frame.remove.all.na.rows(monthly_repeated_measures)) <= 0) {
     message("[WARNING] No monthly-repeated measures found in this set")
     return()
   }
@@ -350,7 +354,7 @@ du.reshape.generate.weekly.repeated <- function(data, dict_kind) {
   matched_columns <- du.match.columns(colnames(data), variables_weekly_repeated_dict$name)
   weekly_repeated_measures <- data[, matched_columns]
 
-  if (nrow(du.data.frame.remove.all.na.rows(weekly_repeated_measures)) <= 0) {
+  if (ncol(weekly_repeated_measures) <= 0 || nrow(du.data.frame.remove.all.na.rows(weekly_repeated_measures)) <= 0) {
     message("[WARNING] No weekly-repeated measures found in this set")
     return()
   }
@@ -429,7 +433,7 @@ du.reshape.generate.trimesterly.repeated <- function(data, dict_kind) {
   matched_columns <- du.match.columns(colnames(data), variables_trimesterly_repeated_dict$name)
   trimesterly_repeated_measures <- data[, matched_columns]
 
-  if (nrow(du.data.frame.remove.all.na.rows(trimesterly_repeated_measures)) <= 0) {
+  if (ncol(trimesterly_repeated_measures) <= 0 || nrow(du.data.frame.remove.all.na.rows(trimesterly_repeated_measures)) <= 0) {
     message("[WARNING] No trimesterly-repeated measures found in this set")
     return()
   }