S3 metadata and file size checks #165
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| Original file line number | Diff line number | Diff line change | ||||
|---|---|---|---|---|---|---|
| @@ -0,0 +1,187 @@ | ||||||
| #' Get available data list from Amazon S3 storage | ||||||
| #' | ||||||
| #' @description | ||||||
| #' | ||||||
| #' Get a table with links to available data files for the specified data version from Amazon S3 storage. | ||||||
| #' | ||||||
| #' @inheritParams spod_available_data | ||||||
| #' @inheritParams global_quiet_param | ||||||
| #' @return A tibble with links, release dates of files in the data, dates of data coverage, local paths to files, and the download status. | ||||||
| #' | ||||||
| #' @keywords internal | ||||||
| spod_available_data_s3 <- function( | ||||||
| ver = c(1, 2), | ||||||
| force = FALSE, | ||||||
| quiet = FALSE, | ||||||
| data_dir = spod_get_data_dir() | ||||||
| ) { | ||||||
| ver <- as.character(ver) | ||||||
| ver <- match.arg(ver) | ||||||
| metadata_folder <- glue::glue("{data_dir}/{spod_subfolder_metadata_cache()}") | ||||||
|
|
||||||
| # if forcing, evict the in-session cache now | ||||||
| if (isTRUE(force)) { | ||||||
| memoise::forget(spod_available_data_s3_memoised) | ||||||
| } | ||||||
|
|
||||||
| # shortcut: if we already have it memoised, return immediately | ||||||
| if (!force && memoise::has_cache(spod_available_data_s3_memoised)(ver)) { | ||||||
| if (!quiet) message("Using memory-cached available data from S3") | ||||||
| return(spod_available_data_s3_memoised(ver)) | ||||||
| } | ||||||
|
|
||||||
| # no in-session data, check your on-disk RDS pool | ||||||
| pattern <- glue::glue("metadata_s3_v{ver}_\\d{{4}}-\\d{{2}}-\\d{{2}}\\.rds$") | ||||||
| rds_files <- fs::dir_ls( | ||||||
| path = metadata_folder, | ||||||
| type = "file", | ||||||
| regexp = pattern | ||||||
| ) |> | ||||||
| sort() | ||||||
|
|
||||||
| latest_file <- utils::tail(rds_files, 1) | ||||||
| latest_date <- if (length(latest_file) == 1) { | ||||||
| stringr::str_extract(basename(latest_file), "\\d{4}-\\d{2}-\\d{2}") |> | ||||||
| as.Date() | ||||||
| } else { | ||||||
| NA | ||||||
| } | ||||||
|
|
||||||
| needs_update <- isTRUE(force) || | ||||||
| length(rds_files) == 0 || | ||||||
| (!is.na(latest_date) && latest_date < Sys.Date()) | ||||||
|
|
||||||
| if (!needs_update) { | ||||||
| if (!quiet) message("Using existing disk cache: ", latest_file) | ||||||
| return(readRDS(latest_file)) | ||||||
| } | ||||||
|
|
||||||
| # if forcing, also clear old disk files | ||||||
| if (isTRUE(force) && length(rds_files) > 0) { | ||||||
| fs::file_delete(rds_files) | ||||||
| } | ||||||
|
|
||||||
| # fetch via the memoised function (this will re-hit S3 if we forgot it) | ||||||
| if (!quiet) message("Fetching latest metadata from AmazonS3 (v", ver, ")...") | ||||||
| dat <- spod_available_data_s3_memoised(ver) | ||||||
|
|
||||||
| # write a new RDS stamped with today's date | ||||||
| file_date <- format(Sys.Date(), "%Y-%m-%d") | ||||||
| out_path <- file.path( | ||||||
| metadata_folder, | ||||||
| glue::glue("metadata_s3_v{ver}_{file_date}.rds") | ||||||
| ) | ||||||
| saveRDS(dat, out_path) | ||||||
| if (!quiet) message("Cached new data to: ", out_path) | ||||||
|
|
||||||
| dat | ||||||
| } | ||||||
|
|
||||||
|
|
||||||
| spod_available_data_s3_function <- function( | ||||||
| ver = c(1, 2) | ||||||
| ) { | ||||||
| ver <- as.character(ver) | ||||||
| ver <- match.arg(ver) | ||||||
|
|
||||||
| bucket <- paste0("mitma-movilidad-v", ver) | ||||||
|
|
||||||
| # original_aws_region <- Sys.getenv("AWS_DEFAULT_REGION") | ||||||
| # original_aws_url_style <- Sys.getenv("AWS_S3_URL_STYLE") | ||||||
| # on.exit({ | ||||||
| # Sys.setenv( | ||||||
| # AWS_DEFAULT_REGION = original_aws_region, | ||||||
| # AWS_S3_URL_STYLE = original_aws_url_style | ||||||
| # ) | ||||||
| # }) | ||||||
| # Sys.setenv( | ||||||
| # AWS_DEFAULT_REGION = "eu-west-1", | ||||||
| # AWS_S3_URL_STYLE = "virtual" | ||||||
| # ) | ||||||
|
|
||||||
| if (ver == 1) { | ||||||
| url_prefix <- "https://opendata-movilidad.mitma.es/" | ||||||
| } else { | ||||||
| url_prefix <- "https://movilidad-opendata.mitma.es/" | ||||||
| } | ||||||
|
|
||||||
| s3 <- paws.storage::s3( | ||||||
| config = list( | ||||||
| credentials = list( | ||||||
| anonymous = TRUE | ||||||
| ) | ||||||
| ) | ||||||
| ) | ||||||
|
|
||||||
| all_objects <- list_objects_v2_all(s3, bucket) | ||||||
|
|
||||||
| # all_objects <- aws.s3::get_bucket_df( | ||||||
| # bucket = bucket, | ||||||
| # prefix = "", # root of bucket | ||||||
| # max = Inf # fetch beyond the default 1000 | ||||||
| # ) | ||||||
|
|
||||||
| all_objects <- all_objects |> | ||||||
| dplyr::as_tibble() |> | ||||||
| dplyr::mutate( | ||||||
| target_url = paste0(url_prefix, .data$Key), | ||||||
| pub_ts = as.POSIXct( | ||||||
| .data$LastModified, | ||||||
| format = "%Y-%m-%dT%H:%M:%OSZ", | ||||||
| tz = "UTC" | ||||||
| ), | ||||||
| file_size_bytes = as.numeric(.data$Size), | ||||||
| etag = gsub('\\"', '', .data$ETag) | ||||||
| ) |> | ||||||
| dplyr::select( | ||||||
| .data$target_url, | ||||||
|
Collaborator
There was a problem hiding this comment. Why not
Suggested change
out of interest?
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There was a problem hiding this comment.
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Author
There was a problem hiding this comment. I recall R CMD check complaining about undefined variables in functions and pointing to those tidy-eval column names, unless they are prepended by .data from rlang.
Member
Author
There was a problem hiding this comment. for example, I forgot to fix the function below spod_store_etags <- function() {
available_data <- spod_available_data(1, check_local_files = TRUE)
available_data <- available_data |>
dplyr::filter(downloaded == TRUE)
local_etags <- available_data$local_path |>
purrr::map_chr(~ spod_compute_s3_etag(.x), .progress = TRUE)
available_data <- available_data |>
dplyr::mutate(local_etag = local_etags) |>
dplyr::as_tibble()
return(available_data)
}I get: Then if I prepend dplyr::filter(!!downloaded == TRUE)Same NOTE: Then replacing the problematic line with: dplyr::filter(.data$downloaded == TRUE)No notes anymore 🤷♂️
Collaborator
There was a problem hiding this comment. Yeah, that's a fair reason for using the I think messages like this Can be resolved with |
||||||
| .data$pub_ts, | ||||||
| .data$file_size_bytes, | ||||||
| .data$etag | ||||||
| ) | ||||||
|
|
||||||
| return(all_objects) | ||||||
| } | ||||||
|
|
||||||
| spod_available_data_s3_memoised <- memoise::memoise( | ||||||
| spod_available_data_s3_function | ||||||
| ) | ||||||
|
|
||||||
| list_objects_v2_all <- function(s3, bucket, prefix = "", max_keys = 10000) { | ||||||
| pages <- paws.storage::paginate( | ||||||
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|
||||||
| s3$list_objects_v2( | ||||||
| Bucket = bucket, | ||||||
| Prefix = prefix, | ||||||
| MaxKeys = max_keys | ||||||
| ), | ||||||
| PageSize = max_keys | ||||||
| ) | ||||||
|
|
||||||
| all_objects <- unlist( | ||||||
| lapply(pages, `[[`, "Contents"), | ||||||
| recursive = FALSE | ||||||
| ) | ||||||
|
|
||||||
| metadata <- dplyr::tibble( | ||||||
| Key = vapply(all_objects, `[[`, character(1), "Key"), | ||||||
| LastModified = as.POSIXct( | ||||||
| vapply(all_objects, `[[`, numeric(1), "LastModified"), | ||||||
| origin = "1970-01-01", | ||||||
| tz = "UTC" | ||||||
| ), | ||||||
| Size = vapply(all_objects, `[[`, numeric(1), "Size"), | ||||||
| ETag = vapply(all_objects, `[[`, character(1), "ETag") | ||||||
| ) | ||||||
|
|
||||||
| # S3 generate download urls | ||||||
| # urls <- metadata$Key |> | ||||||
| # purrr::map( | ||||||
| # ~ s3$generate_presigned_url( | ||||||
| # client_method = "get_object", | ||||||
| # params = list(Bucket = "mitma-movilidad-v1", Key = .x) | ||||||
| # ), | ||||||
| # .progress = TRUE | ||||||
| # ) | ||||||
|
|
||||||
| return(metadata) | ||||||
| } | ||||||
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