From 712ec90bc9596f6dee3147553efe5c93df777bbd Mon Sep 17 00:00:00 2001
From: Ruben Perez Perez <ruben.perper@gmail.com>
Date: Thu, 27 Jul 2023 10:13:35 +0200
Subject: [PATCH] remove deprecated code, fix: https to http for emof join to
 work

---
 R/checkdataset.R   | 23 ++++++++++++++---------
 R/smallfunctions.R |  5 +++--
 2 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/R/checkdataset.R b/R/checkdataset.R
index 75de835..09a4b26 100644
--- a/R/checkdataset.R
+++ b/R/checkdataset.R
@@ -57,6 +57,8 @@ 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)
@@ -64,7 +66,7 @@ checkdataset = function(Event = NULL, Occurrence = NULL, eMoF = NULL, IPTreport
     
   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
index e076870..f3f9675 100644
--- 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 ){