remove deprecated code, fix: https to http for emof join to work

EMODnet · Jul 27, 2023 · 712ec90 · 712ec90
1 parent 1f85a4d
commit 712ec90
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Showing 2 changed files with 17 additions and 11 deletions.
diff --git a/R/checkdataset.R b/R/checkdataset.R
@@ -57,14 +57,16 @@ checkdataset = function(Event = NULL, Occurrence = NULL, eMoF = NULL, IPTreport
 
   if (  exists("Occurrence") == TRUE ) {
 
+   if (!is.null(Occurrence)){
+
     if(!"occurrenceID" %in% names(Occurrence) & "id" %in% names(Occurrence)) {
       warning("There is no occurrenceID field in the Occurrence table; occurrenceID created from id field")
       Occurrence <- Occurrence %>% mutate(occurrenceID = id)
     }
 
   Occurrence <- Occurrence %>% cleandataframe()
 
-  }
+  }}
 
   # Occurrence <- Occurrence %>% mutate_all(na_if, 'NA') %>%
   #                              mutate_all(na_if, '') %>%
@@ -110,16 +112,19 @@ checkdataset = function(Event = NULL, Occurrence = NULL, eMoF = NULL, IPTreport
 
       eMoF <- eMoF %>% cleandataframe()
 
-      # eMoF <- eMoF %>% mutate_all(na_if, 'NA') %>%
-      #                  mutate_all(na_if, '') %>%
-      #                  mutate_all(na_if, ' ')
-      # eMoF <- eMoF[,colSums(is.na(eMoF))<nrow(eMoF)]
+
       eMoF <- fncols(eMoF, c("occurrenceID", "measurementType", "measurementTypeID","measurementValueID", "measurementValue", "measurementUnitID", "eventID", "measurementUnit"))
-      #       eMoF[eMoF =='NA' | eMoF =='' | eMoF ==' '] <- NA
+
+
+      eMoF <- eMoF %>% mutate (measurementTypeID = if_else(str_sub(measurementTypeID, -1, -1)=='/',measurementTypeID, paste(measurementTypeID, "/",  sep = '')),
+                               measurementValueID = if_else(str_sub(measurementValueID, -1, -1)=='/',measurementValueID, paste(measurementValueID, "/",  sep = '')),
+                               measurementUnitID = if_else(str_sub(measurementUnitID, -1, -1)=='/',measurementUnitID, paste(measurementUnitID, "/",  sep = '')),
+                               measurementTypeID = str_replace(measurementTypeID, "https://", "http://"),
+                               measurementValueID = str_replace(measurementValueID, "https://", "http://"),
+                               measurementUnitID = str_replace(measurementUnitID, "https://", "http://")
+
+      )
 
-      eMoF <- eMoF %>% mutate (measurementTypeID = if_else(str_sub(measurementTypeID, -1, -1)=='/',measurementTypeID, paste(measurementTypeID, "/",  sep = '') ),
-                               measurementValueID = if_else(str_sub(measurementValueID, -1, -1)=='/',measurementValueID, paste(measurementValueID, "/",  sep = ''))
-      ) 
 
       if ( exists("Event") == TRUE){
         if(!is.null(eMoF$eventID) == FALSE){

diff --git a/R/smallfunctions.R b/R/smallfunctions.R
@@ -69,18 +69,19 @@ leftfrom <- function(x, y, n = 0) {
 
 cleandataframe <- function (x, vector = TRUE) {
 
+  # format to ISO 8601 if class POSIXct
   for (field in colnames(x)){
     if(TRUE %in% (class(x[[field]]) == "POSIXct")){
       x[[field]] <- format_iso_8601(x[[field]])
     }
-   # format to ISO 8601 if class POSIXct
   }
 
+  # turn character NAs and spaces into an actual empty cell
   x <- x %>% mutate(across(where(is.character), ~na_if(., "NA"))) %>%
              mutate(across(where(is.character), ~na_if(., ""))) %>%
              mutate(across(where(is.character), ~na_if(., " ")))
 
-
+  # remove empty columns
   x <- x[,colSums(is.na(x))<nrow(x)]
 
   if (vector == TRUE ){