check fbapp errors - fbapp2json

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: fbcheck
 Title: Web Interface for Data Quality and Processing
-Version: 2.0.3
+Version: 2.0.4
 Authors@R: c(
         person("Omar","Benites",,"[email protected]",c("aut","cre"))
         )

R/check_error.R

@@ -0,0 +1,52 @@
+
+#' Check error in FieldbookApp data
+#' 
+#' @param dfr data frame. FieldbookApp data.
+#' @description FieldbookApp data is captured by mobiles phones or tablets. After exporting this information, it should be read in R
+#' in order to process, check and curate.
+#' @author Omar Benites
+#' @export
+
+
+check_fbapp <- function(dfr){
+
+  #Solgenomic headers
+  sol_headers<- c("plot_name", "plot_id", "block_number", "plot_number", "rep_number" , "row_number", "col_number",
+                  "accession_name",  "is_a_control", "synosyms", "trial_name", "location_name", "year", "pedigree",
+                  "tier", "seedlot_name", "seed_transaction_operator", "num_seed_per_plot", "range_number", "plot_geo_json",
+                  "timestamp",	"person"	,"location",	"number")
+
+  if(nrow(dfr)){
+    message <- paste("The file is empty")
+    status <- "error"
+  } else if(!is.element("plot_id", fb_headers)){ #Check #1
+    message <- paste("The variable 'plot_id' is missing. Must be included in order to upload into the database")
+    status <- "error"
+  } else if(sum(names(exp_cols) %in% sol_headers) != length(names(exp_cols))) {
+
+    #fieldbook headers
+    fb_headers <- names(dfr)
+
+    #Crop Ontology (CO) headers
+    co_h_lg <- grepl(pattern = "CO", fb_headers) #logical exp. to detect co_headers
+    co_cols <- dfr[co_h_lg] #detect Crop ontology columns 
+
+    #Experiment columns: -get rid trait variables and retain experimental variables (plot, rep, year, etc)
+    exp_cols <- dfr[!co_h_lg]
+
+    #ToDo: create two functions for check ontology terms (exist) and exp sol_headers
+    check_headers <- names(exp_cols) %in% sol_headers  
+
+    #Check #2
+    non_found<- names(exp_cols)[!check_headers]
+    message <- paste("The variable(s)", non_found, "was (were) not found in the database. Refine your file before processing.")
+    status <- "error"
+  } else { #Check #3
+    msg <-  paste("Successfully checked!")
+    status <- "success"
+  }
+
+  out<- list(msg= msg, status=status)
+
+}
+