Minor fixes to print.traits.build

NEWS.md

@@ -13,4 +13,5 @@
 - `summarise_trait_means` will trigger warning due to uninformed calculations
 - Added new function `extract_data`
 - Added new function `bind_databases`
-- Added new function `flatten_databases`
+- Added new function `flatten_databases`
+- Updated print function `print.traits.build`

R/check_compatibility.R

@@ -29,10 +29,7 @@ check_compatibility <- function(database, single_table_allowed = FALSE) {
     } else {
 
       compiled_by_traits.build <-
-        database$metadata$related_identifiers %>% 
-        convert_list_to_df2() %>%
-        dplyr::filter(relation_type == "isCompiledBy") %>% 
-        dplyr::filter(stringr::str_detect(identifier, "github.com/traitecoevo/traits.build"))
+        get_compiled_by_traits.build(database)
 
       if(is.null(compiled_by_traits.build) | nrow(compiled_by_traits.build) > 0) {
         compatible <- TRUE
@@ -67,4 +64,18 @@ check_traits_compatibility <- function(trait_data){
     compatible <- FALSE
 
   invisible(compatible)
+}
+
+
+#' Retrieve compiled by information from metadata table
+#'
+#' @param database traits.build database
+#'
+#' @return logical, TRUE indicating version traits table came from traits.build version > 1.0
+
+get_compiled_by_traits.build <- function(database){
+  database$metadata$related_identifiers %>% 
+  convert_list_to_df2() %>%
+  dplyr::filter(relation_type == "isCompiledBy") %>% 
+  dplyr::filter(stringr::str_detect(identifier, "github.com/traitecoevo/traits.build"))
 }

R/print.austraits.R → R/print.traits.build.R

@@ -8,21 +8,30 @@
 #' @export
 
 print.traits.build <- function(x, ...){
-  # browser()
-  # Setting up
+
+  # Setting up printing information
   version <- x$build_info$version %>% as.character()
   nrecords <- nrow(x$traits)
   nspecies <- unique(x$traits$taxon_name) %>% length()
   ntraits <- unique(x$traits$trait_name) %>% length()
 
 
-  if(package_version(version) < '5.0.0'){
+  if(check_compatibility(x)){
+    database_name <- x$metadata$title
 
-    # Setting up
-    database_name <- x$definitions$austraits$description
-
-    fun <- function() {
-      cli::cli_h1("This database contains a total of {nrecords} records, for {nspecies} taxa and {ntraits} traits.")
+    traits.build_version <- x$metadata$related_identifiers |> 
+      convert_list_to_df2() |> 
+      dplyr::filter(resource_type == "software") |> 
+      dplyr::pull(version)
+
+    nice_summary_output <- function() {
+      cli::cli_h1("This is {version} of {database_name}!")
+
+      cli::cli_bullets(c(
+        "i" = "This database is built using traits.build version {traits.build_version}",
+        "i" = "This database contains a total of {nrecords} records, for {nspecies} taxa and {ntraits} traits."
+      )
+      )
 
       cli::cli_h2("This object is a 'list' with the following components:")
       cli::cli_div(theme = list(span.emph = list(color = "forestgreen")))
@@ -34,32 +43,24 @@
       cli::cli_li("{.emph excluded_data}: A table of data that did not pass quality test and so were excluded from the master dataset.")
       cli::cli_li("{.emph taxonomic_updates}: A table of all taxonomic changes implemented in the construction of AusTraits. Changes are determined by comapring against the APC (Australian Plant Census) and APNI (Australian Plant Names Index).")
       cli::cli_li("{.emph taxa}: A table containing details on taxa associated with information in `traits`. This information has been sourced from the APC (Australian Plant Census) and APNI (Australian Plant Names Index) and is released under a CC-BY3 license.")
-      cli::cli_li("{.emph definitions}: A copy of the definitions for all tables and terms. Information included here was used to process data and generate any documentation for the study.")
       cli::cli_li("{.emph contributors}: A table of people contributing to each study.")
       cli::cli_li("{.emph sources}: Bibtex entries for all primary and secondary sources in the compilation.")
-      cli::cli_li("{.emph build_info}:  A description of the computing environment used to create this version of the dataset, including version number, git commit and R session_info.")
+      cli::cli_li("{.emph definitions}: A copy of the definitions for all tables and terms. Information included here was used to process data and generate any documentation for the study.")
+      cli::cli_li("{.emph schema}: A copy of the schema for all tables and terms. Information included here was used to process data and generate any documentation for the study.")
+      cli::cli_li("{.emph metadata}: Metadata associated with the dataset, including title, creators, license, subject, funding sources.")
+      cli::cli_li("{.emph build_info}: A description of the computing environment used to create this version of the dataset, including version number, git commit and R session_info.")
       cli::cli_end()
 
       cli::cli_alert_info("To access a component, try using the $ e.g. austraits$traits")
     }
 
-    fun()
-  } else{
-    database_name <- x$metadata$title
-
-    traits.build_version <- x$metadata$related_identifiers |> 
-      convert_list_to_df2() |> 
-      dplyr::filter(resource_type == "software") |> 
-      dplyr::pull(version)
+    nice_summary_output()
+  } else { # If not compatible (i.e. old version of database)
+    # Setting up
+    database_name <- x$definitions$austraits$description
 
-    fun <- function() {
-            cli::cli_h1("This is {version} of {database_name}!")
-
-      cli::cli_bullets(c(
-        "i" = "This database is built using traits.build version {traits.build_version}",
-        "i" = "This database contains a total of {nrecords} records, for {nspecies} taxa and {ntraits} traits."
-      )
-      )
+    old_version_nice_output <- function() {
+      cli::cli_h1("This database contains a total of {nrecords} records, for {nspecies} taxa and {ntraits} traits.")
 
       cli::cli_h2("This object is a 'list' with the following components:")
       cli::cli_div(theme = list(span.emph = list(color = "forestgreen")))
@@ -71,18 +72,16 @@
       cli::cli_li("{.emph excluded_data}: A table of data that did not pass quality test and so were excluded from the master dataset.")
       cli::cli_li("{.emph taxonomic_updates}: A table of all taxonomic changes implemented in the construction of AusTraits. Changes are determined by comapring against the APC (Australian Plant Census) and APNI (Australian Plant Names Index).")
       cli::cli_li("{.emph taxa}: A table containing details on taxa associated with information in `traits`. This information has been sourced from the APC (Australian Plant Census) and APNI (Australian Plant Names Index) and is released under a CC-BY3 license.")
+      cli::cli_li("{.emph definitions}: A copy of the definitions for all tables and terms. Information included here was used to process data and generate any documentation for the study.")
       cli::cli_li("{.emph contributors}: A table of people contributing to each study.")
       cli::cli_li("{.emph sources}: Bibtex entries for all primary and secondary sources in the compilation.")
-      cli::cli_li("{.emph definitions}: A copy of the definitions for all tables and terms. Information included here was used to process data and generate any documentation for the study.")
-      cli::cli_li("{.emph schema}: A copy of the schema for all tables and terms. Information included here was used to process data and generate any documentation for the study.")
-      cli::cli_li("{.emph metadata}: Metadata associated with the dataset, including title, creators, license, subject, funding sources.")
-      cli::cli_li("{.emph build_info}: A description of the computing environment used to create this version of the dataset, including version number, git commit and R session_info.")
+      cli::cli_li("{.emph build_info}:  A description of the computing environment used to create this version of the dataset, including version number, git commit and R session_info.")
       cli::cli_end()
 
       cli::cli_alert_info("To access a component, try using the $ e.g. austraits$traits")
     }
 
-    fun()
+    old_version_nice_output()
   }
 }