Move all state variables into environment within package #43

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Merged

atharvashahane28 merged 20 commits into main from feature/39-config-env

Sep 26, 2025

DESCRIPTION

-Original file line number
+Diff line change
@@ Expand Up / @@ -13,7 +13,8 @@ Imports: @@
         plumber,
         jsonlite,
         aws.s3,
-        terra
+        terra,
+        sf
     Suggests:
         testthat (>= 3.0.0),
         callthat,
@@ Expand Down @@

R/flow.R

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -1,28 +1,3 @@
  
    #' Set S3 configuration explicitly

    #'

    #' Allows user to set S3 credentials and bucket at runtime. If not set, environment variables or IAM role will be used.

    set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, bucket = NULL) {

      assign(".s3_config", list(

        access_key = access_key,

        secret_key = secret_key,

        region = region,

        bucket = bucket

      ), envir = .GlobalEnv)

    }

    #' Get S3 configuration from explicit config, environment variables, or IAM role

    get_s3_config <- function() {

      config <- if (exists(".s3_config", envir = .GlobalEnv)) get(".s3_config", envir = .GlobalEnv) else list()

      access_key <- config$access_key %||% Sys.getenv("AWS_ACCESS_KEY_ID", unset = NA)

      secret_key <- config$secret_key %||% Sys.getenv("AWS_SECRET_ACCESS_KEY", unset = NA)

      region     <- config$region     %||% Sys.getenv("AWS_DEFAULT_REGION", unset = NA)

      bucket     <- config$bucket     %||% Sys.getenv("S3_BUCKET_NAME", unset = NA)

      list(access_key = access_key, secret_key = secret_key, region = region, bucket = bucket)

    }

    #' Null coalescing operator for config values

    `%||%` <- function(a, b) if (!is.null(a) && !is.na(a) && nzchar(a)) a else b

    if(FALSE) {

       # Manually set function arguments for dev and debugging

       # Running code here allows running function body code outside of the

    @@ -92,11 +67,6 @@ save_local_path <- "config/save_local.flag"
  
    #'    `type`

    #' @export

    flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE) {

      # TODO:

      # utils::data("species", package = "BirdFlowAPI", envir = environment())

      # load_models()

      s3_cfg <- get_s3_config()

      s3_enabled <- !is.na(s3_cfg$bucket) && nzchar(s3_cfg$bucket)

    @@ -110,7 +80,9 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
  
      }

      log_progress <- function(msg) {

        cat(sprintf("[%s] %s\n", Sys.time(), msg), file = "./flow_debug.log", append = TRUE)

        if(s3_cfg$log) {

          cat(sprintf("[%s] %s\n", Sys.time(), msg), file = s3_cfg$log_file_path, append = TRUE)

        }

      }

      log_progress(paste0("Starting flow function with arguments: loc=", loc, ", week=", week, ", taxa=", taxa, ", n=", n, ", direction=", direction, ", save_local=", save_local))

    @@ -157,11 +129,12 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
  
      pred_weeks <- BirdFlowR::lookup_timestep_sequence(bf, start = week, n = n, direction = direction)

      png_files <- paste0(flow_type, "_", taxa, "_", pred_weeks, ".png")

      symbology_files <- paste0(flow_type, "_", taxa, "_", pred_weeks, ".json")

      png_bucket_paths <- paste0(s3_flow_path, cache_prefix, png_files)

      symbology_bucket_paths <- paste0(s3_flow_path, cache_prefix, symbology_files)

      png_urls <- paste0(s3_flow_url, cache_prefix, png_files)

      symbology_urls <- paste0(s3_flow_url, cache_prefix, symbology_files)

      tiff_bucket_path <- paste0(s3_flow_path, cache_prefix, flow_type, "_", taxa, ".tif")

      png_bucket_paths <- paste0(s3_cfg$s3_flow_path, cache_prefix, png_files)

      symbology_bucket_paths <- paste0(s3_cfg$s3_flow_path, cache_prefix, symbology_files)

      png_urls <- paste0(s3_cfg$s3_flow_url, cache_prefix, png_files)

      symbology_urls <- paste0(s3_cfg$s3_flow_url, cache_prefix, symbology_files)

      tiff_bucket_path <- paste0(s3_cfg$s3_flow_path, cache_prefix, flow_type, "_", taxa, ".tif")

      local_temp_path <- s3_cfg$local_temp_path

      # --- CACHE CHECK BLOCK ---

      cache_hit <- TRUE

    @@ -177,9 +150,9 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
  
        tiff_exists <- aws.s3::object_exists(object = tiff_bucket_path, bucket = s3_cfg$bucket)

        if (!tiff_exists) cache_hit <- FALSE

      } else {

        # Local cache: check if all files exist in localtmp

        dir.create("localtmp", showWarnings = FALSE)

        local_cache_prefix <- file.path("localtmp", gsub("/", "_", cache_prefix))

        # Local cache: check if all files exist in local_temp_path

        dir.create(local_temp_path, showWarnings = FALSE)

        local_cache_prefix <- file.path(local_temp_path, gsub("/", "_", cache_prefix))

        png_local_paths <- file.path(local_cache_prefix, png_files)

        json_local_paths <- file.path(local_cache_prefix, symbology_files)

        tiff_local_path <- file.path(local_cache_prefix, paste0(flow_type, "_", taxa, ".tif"))

    @@ -198,22 +171,22 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
  
          )

          log_progress(paste0("Cached result for week ", pred_weeks[i], ": url=", result[[i]]$url, ", legend=", result[[i]]$legend))

        }

        log_progress(if (save_local) "Returned cached result from localtmp" else "Returned cached result from S3")

        log_progress(if (save_local) "Returned cached result from local_temp_path" else "Returned cached result from S3")

        return(

          list(

            start = list(week = week, taxa = taxa, loc = loc),

            status = "cached",

            result = result,

            geotiff = if (save_local) tiff_local_path else paste0(s3_flow_url, cache_prefix, flow_type, "_", taxa, ".tif")

            geotiff = if (save_local) tiff_local_path else paste0(s3_cfg$s3_flow_url, cache_prefix, flow_type, "_", taxa, ".tif")

          )

        )

      }

      # --- END CACHE CHECK BLOCK ---

      # Continue with prediction

      if (save_local || !s3_enabled) {

        dir.create("localtmp", showWarnings = FALSE)

        out_path <- file.path("localtmp", gsub("/", "_", cache_prefix))

        dir.create(local_temp_path, showWarnings = FALSE)

        out_path <- file.path(local_temp_path, gsub("/", "_", cache_prefix))

        dir.create(out_path, recursive = TRUE, showWarnings = FALSE)

      } else {

        out_path <- tempfile(pattern = "flow_", tmpdir = "/dev/shm")

    @@ -265,25 +238,25 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
  
      log_progress("Projecting and cropping raster for web output.")

      log_progress(paste0("combined class: ", class(combined)))

      log_progress(paste0("ai_app_crs$input: ", ai_app_crs$input))

      log_progress(paste0("ai_app_extent: ", ai_app_extent))

      log_progress(paste0("s3_cfg$ai_app_crs$input: ", s3_cfg$ai_app_crs$input))

      log_progress(paste0("s3_cfg$ai_app_extent: ", s3_cfg$ai_app_extent))

      if (is.null(combined) || !inherits(combined, "SpatRaster")) {

        log_progress("ERROR: combined raster is NULL or not a SpatRaster. Aborting.")

        return(format_error("combined raster is NULL or not a SpatRaster"))

      }

      if (is.null(ai_app_crs$input)) {

        log_progress("ERROR: ai_app_crs$input is NULL. Aborting.")

        return(format_error("ai_app_crs$input is NULL"))

      if (is.null(s3_cfg$ai_app_crs$input)) {

        log_progress("ERROR: s3_cfg$ai_app_crs$input is NULL. Aborting.")

        return(format_error("s3_cfg$ai_app_crs$input is NULL"))

      }

      if (is.null(ai_app_extent)) {

        log_progress("ERROR: ai_app_extent is NULL. Aborting.")

        return(format_error("ai_app_extent is NULL"))

      if (is.null(s3_cfg$ai_app_extent)) {

        log_progress("ERROR: s3_cfg$ai_app_extent is NULL. Aborting.")

        return(format_error("s3_cfg$ai_app_extent is NULL"))

      }

      log_progress("Projecting")

      web_raster <- combined |> terra::project(ai_app_crs$input)

      web_raster <- combined |> terra::project(s3_cfg$ai_app_crs$input)

      log_progress("Cropping")

      web_raster <- terra::crop(web_raster, ai_app_extent)

      web_raster <- terra::crop(web_raster, s3_cfg$ai_app_extent)

      log_progress("Done cropping")

      png_paths <- file.path(out_path, png_files)

      symbology_paths <- file.path(out_path, symbology_files)

    @@ -371,7 +344,7 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
  
          start = list(week = week, taxa = taxa, loc = loc),

          status = "success",

          result = result,

          geotiff = if (save_local) tiff_path else paste0(s3_flow_url, cache_prefix, flow_type, "_", taxa, ".tif")

          geotiff = if (save_local) tiff_path else paste0(s3_cfg$s3_flow_url, cache_prefix, flow_type, "_", taxa, ".tif")

        )

      )

    }

R/globals.R

This file was deleted.

R/s3_config.R

-Original file line number
+Diff line change
@@ -0,0 +1,46 @@
+    s3_config <- new.env()
+    set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, bucket = NULL, log = TRUE, log_file_path = "./flow_debug.log", local_temp_path = "localtmp") {
+      s3_config$access_key <- access_key
+      s3_config$secret_key <- secret_key
+      s3_config$region <- region
+      s3_config$bucket <- bucket
+      s3_config$ai_app_crs <- sf::st_crs("EPSG:3857")
+      s3_config$ai_app_extent <- c(-18924313.4348565, -5565974.53966368, 1118889.97485796, 15538711.0963092)
+      s3_config$s3_bucket_name <- "avianinfluenza"
+      s3_config$s3_flow_path <- "flow/"
+      s3_config$s3_flow_url <- "https://avianinfluenza.s3.us-east-2.amazonaws.com/flow/"
+      s3_config$local_cache <- tempdir()
+      if(!file.exists(s3_config$local_cache))
+        dir.create(s3_config$local_cache)
+      s3_config$log <- log
+      s3_config$log_file_path <- log_file_path
+      s3_config$local_temp_path <- local_temp_path
+    }
+    get_s3_config <- function() {
+      list(
+        access_key = s3_config$access_key %||% Sys.getenv("AWS_ACCESS_KEY_ID", unset = NA),
+        secret_key = s3_config$secret_key %||% Sys.getenv("AWS_SECRET_ACCESS_KEY", unset = NA),
+        region = s3_config$region %||% Sys.getenv("AWS_DEFAULT_REGION", unset = NA),
+        bucket = s3_config$bucket %||% Sys.getenv("S3_BUCKET_NAME", unset = NA),
+        ai_app_crs = s3_config$ai_app_crs %||% NA,
+        ai_app_extent = s3_config$ai_app_extent %||% NA,
+        s3_bucket_name = s3_config$s3_bucket_name %||% NA,
+        s3_flow_path = s3_config$s3_flow_path %||% NA,
+        s3_flow_url = s3_config$s3_flow_url %||% NA,
+        local_cache = s3_config$local_cache %||% NA,
+        log = s3_config$log %||% NA,
+        log_file_path = s3_config$log_file_path %||% NA,
+        local_temp_path = s3_config$local_temp_path %||% NA
+      )
+    }
+    `%||%` <- function(a, b) {
+      if (is.null(a)) return(b)
+      if (is.atomic(a) && length(a) == 1 && is.na(a)) return(b)
+      if (is.character(a) && length(a) == 1 && !nzchar(a)) return(b)
+      a
+    }

man/get_s3_config.Rd

This file was deleted.

man/grapes-or-or-grapes.Rd

This file was deleted.

man/set_s3_config.Rd

This file was deleted.

tests/testthat/setup.R

-Original file line number
+Diff line change
@@ -1 +1,2 @@
-    load_models()
+    load_models()
+    set_s3_config()

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