Add fish as food pipeline

fishAsFood/_targets.R

+library(targets)
+
+options(tidyverse.quiet = TRUE)
+tar_option_set(packages = c("tidyverse", 
+                            "readxl",
+                            "jsonlite"))
+
+source('src/data_utils.R')
+
+p0 <- list(
+  tar_target(
+    p0_sb_id,
+    '644ae0e0d34e45f6ddccf773'
+  )
+)
+
+p1 <- list(
+  tar_target(
+    p1_data_xlsx,
+    {
+      data_file <- 'Rec fish food_20230509_for USGS data release.xlsx'
+      out_file <- file.path('in', data_file)
+      sbtools::item_file_download(sb_id = p0_sb_id, 
+                                  names = data_file, 
+                                  destinations = out_file)
+      return(out_file)
+    },
+    format = 'file'
+  )
+)
+
+p2 <- list(
+  tar_target(
+    p2_data,
+    clean_input_data(data_file = p1_data_xlsx)
+  ),
+  tar_target(
+    p2_price_json,
+    build_nested_json(
+      data = p2_data, 
+      focal_columns = c('name' = 'admin', 'value' = 'total_value_species'), 
+      out_file = '../public/total_price.json'
+    ),
+    format = 'file'
+  )
+)
+
+c(p0, p1, p2)

fishAsFood/src/data_utils.R

+clean_input_data <- function(data_file) {
+  data <- read_xlsx(data_file, na="NA")
+  
+  names(data)<-make.names(names(data),unique = TRUE)
+  
+  data |>
+    mutate(
+      family = ifelse(family == 'Salmonindae', 'Salmonidae', family),
+      species_common = ifelse(species_common == 'Bey?ehir bleak', 
+                              'Beyşehir bleak', 
+                              species_common)
+      )
+}
+
+build_nested_json <- function(data, focal_columns, out_file) {
+  data_list <- data |>
+    filter(!is.na(focal_columns[['value']])) |>
+    group_by(name = family) |>
+    group_modify(~ {
+      species_list <- .x |> 
+        group_by(name = species_common) |>
+        group_modify(~ {
+          country_list <- .x |>
+            select(!!focal_columns) |>
+            split(nrow(.x))
+          return(tibble('children' = country_list))
+        })
+      return(tibble('children' = list(species_list)))
+    })
+  
+  json_data <- jsonlite::toJSON(data_list, auto_unbox = TRUE, pretty = TRUE)
+  json_data <- paste0('{\n "name": "fish", "children":', json_data, '\n}')
+  write(json_data, file = out_file)
+  
+  return(out_file)
+}
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