Abstract metadata caching to helper functions and store cached metata…

…data as list

Also cache media metadata. Relates to #57 and #58

R/ala_counts.R

@@ -122,9 +122,11 @@ ala_counts <- function(taxa = NULL, filters = NULL, locations = NULL, group_by,
     )
   }
   names(counts) <- c(group_by, "count")
+  attr(counts, "data_type") <- "counts"
 
   if (caching) {
-    saveRDS(counts, cache_file)
+    write_cache_file(object = counts, data_type = "occurrences", query = list(),
+                     cache_file = cache_file)
   }
 
   return(counts)

R/ala_media.R

@@ -55,6 +55,7 @@ ala_media <- function(taxa = NULL, filters = NULL, locations = NULL,
   image_url <- server_config("images_base_url")
 
   verbose <- getOption("galah_config")$verbose
+  caching <- getOption("galah_config")$caching
   assert_that(!missing(download_dir),
   msg = "A path to an existing directory to download images to is required")
   assert_that(file.exists(download_dir))
@@ -64,6 +65,16 @@ ala_media <- function(taxa = NULL, filters = NULL, locations = NULL,
     warning("No filters have been provided. All images and sounds will be downloaded.")
   }
 
+  if (caching) {
+    cache_file <- cache_filename(
+      "media",
+      unlist(build_query(taxa, filters, locations, columns))
+    )
+    if (file.exists(cache_file)) {
+      return(read_cache_file(cache_file))
+    }
+  }
+
   # Check whether any of the filters are media-specific filters and
   # filter to records with image/sound/video
   media_filters <- filters[filters$name %in% search_fields(type = "media")$id,]
@@ -133,6 +144,11 @@ ala_media <- function(taxa = NULL, filters = NULL, locations = NULL,
   if (verbose) {
     message("\n",nrow(all_data), " files were downloaded to ", download_dir)
   }
+  attr(all_data, "data_type") <- "media"
+  if (caching) {
+    write_cache_file(object = all_data, data_type = "media", query = list(),
+                     cache_file = cache_file)
+  }
   return(all_data)
 }
 

R/ala_occurrences.R

@@ -114,9 +114,11 @@ no valid column names have been provided. To check whether column names are vali
   # add DOI as attribute
   attr(df, "doi") <- get_doi(mint_doi, data_path)
   attr(df, "search_url") <- download_resp$search_url
-
+  attr(df, "data_type") <- "occurrences"
+
   if (caching) {
-    saveRDS(df, file = cache_file)
+    write_cache_file(object = df, data_type = "occurrences", query = list(),
+                     cache_file = cache_file)
   }
   return(df)
 }

R/ala_species.R

@@ -72,9 +72,11 @@ ala_species <- function(taxa = NULL, filters = NULL, locations = NULL) {
                        cache_file = tmp)
   # overwrite file with fixed names
   names(data) <- rename_columns(names(data), type = "checklist")
-
+  attr(data, "data_type") <- "species"
+
   if (caching) {
-    saveRDS(data, cache_file)
+    write_cache_file(object = data, data_type = "species", query = list(),
+                     cache_file = cache_file)
   }
   return(data)
 }

R/utilities_internal.R

@@ -251,10 +251,17 @@ check_taxa_arg <- function(taxa) {
 
 # Read cached file
 read_cache_file <- function(filename) {
-  if (getOption("galah_config")$caching) { message("Using cached file") }
+  if (getOption("galah_config")$verbose) { message("Using cached file") }
   readRDS(filename)
 }
 
+# Write file to cache and metadata to metadata cache
+write_cache_file <- function(object, query, data_type, cache_file) {
+  if (getOption("galah_config")$verbose) { message("Writing to cache file") }
+  saveRDS(object, cache_file)
+  write_metadata(query, data_type, cache_file)
+}
+
 # Hash cache filename from argument list
 cache_filename <- function(...) {
   args <- c(...)
@@ -264,14 +271,15 @@ cache_filename <- function(...) {
 
 # Write function call metadata to RDS file to enable metadata viewing with
 # `find_cached_files()`
-write_metadata <- function(cache_file, data_type, query) {
+write_metadata <- function(query, data_type, cache_file) {
   metadata_file <- file.path(getOption("galah_config")$cache_directory,
                              "metadata.rds")
   if (file.exists(metadata_file)) {
     metadata <- readRDS(metadata_file)
   } else {
     metadata <- list()
   }
+  file_id <- str_split(cache_file, "\\.")[[1]][1]
   metadata$`file_id` <- list(data_type = data_type, query = query)
   saveRDS(metadata, metadata_file)
 }