edits public search

added the preset function at the fetch step itself so just needs to be used once
boldsystems-central · Sep 24, 2024 · e8cfc03 · e8cfc03
1 parent 5625bda
commit e8cfc03
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Showing 4 changed files with 29 additions and 34 deletions.
diff --git a/R/external.bold.analyze.diversity.R b/R/external.bold.analyze.diversity.R
@@ -140,18 +140,18 @@ bold.analyze.diversity <- function(bold_df,
 
   # Check if data is a data frame object
 
-  if(is.data.frame(bold_df)==FALSE)
+  if(any(is.data.frame(bold_df)==FALSE,nrow(bold_df)==0))
 
   {
-    stop("Input is not a data frame")
+    stop("Please re-check data input. Input needs to be a non-empty data frame")
   }
 
-  # Check whether the data frame is empty
-
-  if(nrow(bold_df)==0)
+  # Check if taxon_rank is empty
 
+  if(is.null(taxon_rank))
   {
-    stop("Dataframe is empty")
+    ## Taxon rank cannot be empty
+    stop ("Taxon rank cannot be left empty")
   }
 
   # Empty output list

diff --git a/R/external.bold.public.search.R b/R/external.bold.public.search.R
@@ -105,6 +105,7 @@ bold.public.search <- function(taxonomy = NULL,
     if(length(trial_query_input)<=5)
     {
       result = fetch.public.data(query = trial_query_input)
+
     }
 
     else
@@ -133,25 +134,25 @@ bold.public.search <- function(taxonomy = NULL,
       result.post.filter = Filter(function(df) nrow(df) > 0,
                                   result.pre.filter)
 
-      # removing unwanted columns
-
-      result.rem.col=lapply(result.post.filter,
-                            function (df)
-                            {
-                              res=check_and_return_preset_df(df,
-                                                             category = "check_return",
-                                                             preset = public.data.fields)
-                              return(res)
-                            }
-      )
+      # # removing unwanted columns
+      #
+      # result.rem.col=lapply(result.post.filter,
+      #                       function (df)
+      #                       {
+      #                         res=check_and_return_preset_df(df,
+      #                                                        category = "check_return",
+      #                                                        preset = public.data.fields)
+      #                         return(res)
+      #                       }
+      # )
 
 
       # Binding the list of dataframes
 
-      result=result.rem.col%>%
-        bind_rows(.)%>%
-        dplyr::select(processid,
-                      sampleid)
+      result=result.post.filter%>%
+        bind_rows(.)
+        # dplyr::select(processid,
+        #               sampleid)
 
     }
 

diff --git a/R/helper.column_presets.R b/R/helper.column_presets.R
@@ -16,17 +16,7 @@ common_ids<-c("processid","sampleid")
 
 public.data.fields<-bold_fields%>%
   dplyr::select(field)%>%
-  dplyr::filter(field %in% c(common_ids,
-                             "coord",
-                             "inst",
-                             "identified_by",
-                             "sequence_run_site",
-                             "marker_code",
-                             "nuc_basecount",
-                             "collection_date_start",
-                             "collection_date_end",
-                             "elev",
-                             "depth"))
+  dplyr::filter(field %in% c(common_ids))
 
 ## Presets for export and summary
 

diff --git a/R/helper.public.search.public_data.R b/R/helper.public.search.public_data.R
@@ -152,10 +152,14 @@ fetch.public.data<-function (query)
   # final_data.pre=reassign.data.type(final_data)
 
   final_data$collection_date_start<-as.Date(final_data$collection_date_start,format("%Y-%m-%d"))
-  
+
   final_data$collection_date_end<-as.Date(final_data$collection_date_end,format("%Y-%m-%d"))
 
-  return(final_data)
+  final_data_preset=check_and_return_preset_df(final_data,
+                             category = "check_return",
+                             preset = public.data.fields)
+
+  return(final_data_preset)
 
 }