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update_collection.R
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update_collection.R
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options(
finbif_api_url = Sys.getenv("FINBIF_API"),
finbif_use_cache = FALSE,
finbif_use_cache_metadata = TRUE,
finbif_max_page_size = 250L,
finbif_rate_limit = Inf,
finbif_retry_times = 10,
finbif_retry_pause_base = 2,
finbif_retry_pause_cap = 5e3
)
update_collection <- function(
collection,
timeout = 3600,
start_timer = tictoc::tic(),
gbif_datasets = f2g::get_gbif_datasets()
) {
force(start_timer)
archive <- f2g::get_archive_path(collection)
staged_archive <- f2g::stage_archive(archive)
subsets <- f2g::get_subsets(collection)
f2g::write_meta(staged_archive, subsets)
f2g::unstage_archive(staged_archive)
f2g::clean_occurrences(staged_archive, subsets)
any_need_archive <- logical()
for (subset in sample(subsets)) {
file <- f2g::get_file_name(subset)
media_file <- f2g::get_file_name(subset, prefix = "media")
mod_time <- f2g::last_mod(staged_archive, file)
subset_age <- difftime(Sys.time(), mod_time, units = "weeks")
needs_archiving <- subset_age > config::get("max_age_weeks")
if (needs_archiving) {
subset_n <- f2g::count_occurrences(subset)
unequal <- f2g::count_occurrences(staged_archive, file) != subset_n
trigger <- Sys.getenv("TRIGGER")
last_mod_subset <- f2g::last_mod(subset)
use_trigger <- trigger > last_mod_subset
use_trigger <- isTRUE(use_trigger)
if (use_trigger) {
last_mod_subset <- trigger
}
outdated <- as.POSIXct(last_mod_subset) > mod_time
needs_archiving <- any(unequal, outdated)
if (needs_archiving) {
f2g::archive_occurrences(
staged_archive, file, media_file, subset, n = subset_n
)
f2g::unstage_archive(staged_archive)
}
}
any_need_archive <- any(needs_archiving, any_need_archive)
stop_timer <- tictoc::toc(quiet = TRUE)
tictoc::tic()
if (stop_timer$toc - start_timer > timeout) break
}
has_all_subsets <- identical(
length(subsets), f2g::n_archived_subsets(archive)
)
uuid <- NULL
if (has_all_subsets) {
registration <- f2g::get_registration(gbif_datasets, collection)
md <- f2g::get_metadata(collection)
arr <- identical(md[["intellectual_rights"]], "All Rights Reserved")
if (arr) {
message(
sprintf(
"WARNING [%s] Collection %s does not have an open license",
format(Sys.time()),
collection
)
)
}
need_metadata_upd <- f2g::last_mod(collection) > f2g::last_mod(registration)
if (!f2g::skip_gbif(collection) && !arr) {
if (is.null(registration)) {
uuid <- f2g::send_gbif_dataset_metadata(md)
f2g::send_gbif_dataset_endpoint(f2g::get_endpoint(collection), uuid)
f2g::send_gbif_dataset_id(collection, uuid)
} else {
if (isTRUE(need_metadata_upd)) {
f2g::update_gbif_dataset_metadata(md, registration)
}
uuid <- f2g::get_uuid(registration)
f2g::update_gbif_dataset_endpoint(f2g::get_endpoint(collection), uuid)
}
}
f2g::write_eml(staged_archive, collection, uuid, md)
f2g::unstage_archive(staged_archive)
f2g::publish_archive(staged_archive)
ingest <- need_metadata_upd || any_need_archive || is.null(registration)
if (!f2g::skip_gbif(collection) && ingest) {
f2g::initiate_gbif_ingestion(uuid)
}
}
invisible(NULL)
}