Moved URL creation from server to galah_download (#89)

* Code to generate link in processing #87

* Renames Establishment means earlier in workflow to remove processing in server.R

* Moved renaming of voucher location to repository to earlier workflow and out of server. Removed creation of URL from server and directly using link field.

* Suppressed warnings from APCalign #87

* Removed URL creaton in downloadhandler

* Updated snapshot

R/galah_download.R

@@ -166,21 +166,20 @@ retrieve_data <- function(taxon,
 get_establishment_status <- function(ala_cleaned, taxon = taxon) {
   if (taxon == "Plantae") {
     resources <- APCalign::load_taxonomic_resources()
+    suppressWarnings(
     lookup <-
       APCalign::native_anywhere_in_australia(unique(ala_cleaned$Species), resources = resources)
+    )
 
     lookup <- dplyr::rename(lookup, Species = species)
 
     ala_cleaned <-
       ala_cleaned |> dplyr::left_join(lookup, by = dplyr::join_by("Species"))
-
-    return(ala_cleaned)
   }
   if (taxon %in% c("Cicadoidea", "Marsupialia", "Odonata", "Papilionoidea")) {
     ala_cleaned$native_anywhere_in_aus <- "native"
     ala_cleaned$native_anywhere_in_aus[ala_cleaned$Species %in% c("Danaus plexippus", "Pieris rapae")] <-
       "introduced"
-    return(ala_cleaned)
   }
   if (!taxon %in% c("Cicadoidea",
                     "Marsupialia",
@@ -189,6 +188,9 @@ get_establishment_status <- function(ala_cleaned, taxon = taxon) {
                     "Plantae")) {
     ala_cleaned$native_anywhere_in_aus <- "unknown"
   }
+  # Rename native_anywhere_in_aus
+  ala_cleaned <- dplyr::rename(ala_cleaned,"Establishment means" = native_anywhere_in_aus)
+
   return(ala_cleaned)
 }
 
@@ -211,7 +213,7 @@ process_data <- function(data) {
       !stringr::str_detect(species, "spec.$")
     ) |>
     dplyr::mutate(
-      voucher_location = dplyr::if_else(!is.na(references), references, institutionCode),
+      repository = dplyr::if_else(!is.na(references), references, institutionCode),
       voucher_type = dplyr::case_when(
         basisOfRecord == "PRESERVED_SPECIMEN" ~ "Collection",
         !is.na(sounds) ~ "Audio",
@@ -232,10 +234,13 @@ process_data <- function(data) {
       lat,
       long,
       voucher_type,
-      voucher_location,
+      repository,
       recordedBy,
       recordID
     ) |>
+    dplyr::mutate(link = dplyr::case_when(grepl("https", repository) ~ repository,
+                            TRUE ~ paste0("https://biocache.ala.org.au/occurrences/", recordID))
+    ) |> 
     janitor::clean_names("title")
 }
 

R/infinitylists-package.R

@@ -57,6 +57,9 @@ utils::globalVariables(
     "str_detect",
     "voucher_location",
     "voucher_type",
-    "write.csv"
+    "write.csv",
+    "Link", 
+    "Repository",
+    "Establishment means"
   )
 )

R/server.R

@@ -150,7 +150,7 @@ infinity_server <- function(...) {
       total_family <- length(unique(data$Family))
 
       native <-
-        dplyr::filter(data, native_anywhere_in_aus == "native")
+        dplyr::filter(data, `Establishment means` == "native")
       if (nrow(native) > 0)
         total_native_species <- length(unique(native$Species))
       else
@@ -242,7 +242,7 @@ infinity_server <- function(...) {
             N = integer(0),
             Long = numeric(0),
             Lat = numeric(0),
-            `Voucher location` = character(0),
+            `Repository` = character(0),
             `Recorded by` = character(0),
             Native = character(0)
           )
@@ -266,28 +266,27 @@ infinity_server <- function(...) {
         },
         Lat = Lat[1],
         Long = Long[1],
-        `Repository` = ifelse(
-          grepl("https", `Voucher Location`[1]),
+        Repository = ifelse(
+          grepl("https", Repository[1]),
           paste0(
             "<a href='",
-            `Voucher Location`[1],
+            Link[1],
             "' target='_blank'>",
             "iNat",
             "</a>"
           ),
           paste0(
             "<a href='",
-            "https://biocache.ala.org.au/occurrences/",
-            `Record Id`[1],
+            Link[1],
             "' target='_blank'>",
-            `Voucher Location`[1],
+            Repository[1],
             "</a>"
           )
         ),
         `Recorded by` = `Recorded by`[1]
       ),
       by = .(Species,
-             `Establishment means` = native_anywhere_in_aus,
+             `Establishment means`,
              `Voucher type` = `Voucher Type`)]
 
 
@@ -354,25 +353,12 @@ infinity_server <- function(...) {
       },
       content = function(file) {
         data <- intersect_data()
-        data$`Voucher Location` = ifelse(
-          grepl("https", data$`Voucher Location`),
-          data$`Voucher Location`
-          ,
-          paste0(
-            "https://biocache.ala.org.au/occurrences/",
-            data$`Record Id`
-          )
-        )
-        data <-
-          dplyr::rename(data,
-                 'Establishment means' = native_anywhere_in_aus,
-                 'Repository' = `Voucher Location`)
+        # Fixing the date
         collectionDate_partial = lubridate::ymd_hms(data$`Collection Date`, tz = "UTC", quiet = TRUE)
         collectionDate_all = dplyr::if_else(
           is.na(collectionDate_partial),
           lubridate::ymd(data$`Collection Date`, tz = "UTC", quiet = TRUE),
-          collectionDate_partial
-        )
+          collectionDate_partial)
         data$`Collection Date` <-
           paste(
             lubridate::year(collectionDate_all),

tests/testthat/_snaps/galah_download.md

@@ -3,16 +3,16 @@
     Code
       odonata
     Output
-      # A tibble: 7 x 11
-        Species            Genus Family `Collection Date`     Lat  Long `Voucher Type`
-        <chr>              <chr> <chr>  <dttm>              <dbl> <dbl> <chr>         
-      1 Adversaeschna bre~ Adve~ Aeshn~ 1924-10-01 00:00:00 -33.9  151. Collection    
-      2 Diplacodes bipunc~ Dipl~ Libel~ 1924-02-23 00:00:00 -37.8  145. Collection    
-      3 Austrolestes leda  Aust~ Lesti~ 1924-11-06 00:00:00 -28.7  152. Collection    
-      4 Synthemis tasmani~ Synt~ Synth~ 1924-01-01 00:00:00 -41.9  145. Collection    
-      5 Austroaeschna par~ Aust~ Telep~ 1924-02-01 00:00:00 -42.1  145. Collection    
-      6 Hemicordulia tau   Hemi~ Cordu~ 1924-10-10 00:00:00 -28.7  152. Collection    
-      7 Synthemis tasmani~ Synt~ Synth~ 1924-01-01 00:00:00 -41.9  145. Collection    
-      # i 4 more variables: `Voucher Location` <chr>, `Recorded by` <chr>,
-      #   `Record Id` <chr>, native_anywhere_in_aus <chr>
+      # A tibble: 7 x 12
+        Species Genus Family `Collection Date`     Lat  Long `Voucher Type` Repository
+        <chr>   <chr> <chr>  <dttm>              <dbl> <dbl> <chr>          <chr>     
+      1 Advers~ Adve~ Aeshn~ 1924-10-01 00:00:00 -33.9  151. Collection     AM        
+      2 Diplac~ Dipl~ Libel~ 1924-02-23 00:00:00 -37.8  145. Collection     NMV       
+      3 Austro~ Aust~ Lesti~ 1924-11-06 00:00:00 -28.7  152. Collection     QM        
+      4 Synthe~ Synt~ Synth~ 1924-01-01 00:00:00 -41.9  145. Collection     QM        
+      5 Austro~ Aust~ Aeshn~ 1924-02-01 00:00:00 -42.1  145. Collection     QM        
+      6 Hemico~ Hemi~ Cordu~ 1924-10-10 00:00:00 -28.7  152. Collection     QM        
+      7 Synthe~ Synt~ Synth~ 1924-01-01 00:00:00 -41.9  145. Collection     QM        
+      # i 4 more variables: `Recorded by` <chr>, `Record Id` <chr>, Link <chr>,
+      #   `Establishment means` <chr>