enh: update cast-api query getter function

Author: dshemetov

R/aux_data_utils.R

@@ -676,14 +676,14 @@ get_nhsn_data_archive <- function(disease = c("covid", "flu")) {
     signal = glue::glue("confirmed_admissions_{disease}_ew"),
     geo_type = "state",
     columns = c("geo_value", "time_value", "value", "report_ts_nominal_start", "report_ts_nominal_end"),
-    limit = -1
+    version_query = glue::glue("all<={Sys.Date()}")
   )
   nhsn_nation <- get_cast_api_data(
     source = "nhsn",
     signal = glue::glue("confirmed_admissions_{disease}_ew"),
     geo_type = "nation",
     columns = c("geo_value", "time_value", "value", "report_ts_nominal_start", "report_ts_nominal_end"),
-    limit = -1
+    version_query = glue::glue("all<={Sys.Date()}")
   )
   nhsn_data <- nhsn_state %>%
     rbind(nhsn_nation) %>%
@@ -707,14 +707,14 @@ up_to_date_nssp_state_archive <- function(disease = c("covid", "influenza")) {
     signal = glue::glue("pct_ed_visits_{disease}"),
     geo_type = "nation",
     columns = c("geo_value", "time_value", "value", "report_ts_nominal_start", "report_ts_nominal_end"),
-    limit = -1
+    version_query = glue::glue("all<={Sys.Date()}")
   )
   nssp_state <- get_cast_api_data(
     source = "nssp",
     signal = glue::glue("pct_ed_visits_{disease}"),
     geo_type = "state",
     columns = c("geo_value", "time_value", "value", "report_ts_nominal_start", "report_ts_nominal_end"),
-    limit = -1
+    version_query = glue::glue("all<={Sys.Date()}")
   )
   nssp_data <- nssp_state %>%
     rbind(nssp_national) %>%

R/utils.R

@@ -941,33 +941,26 @@ compare_s3_etag <- function(bucket, key, region = "us-east-1") {
 }
 
 build_cast_api_query <- function(
-    source = c("nssp", "nhsn"),
-    signal = NULL,
-    geo_type = c("state", "nation"),
+    source,
+    signal,
+    geo_type,
     columns = NULL,
     fill_method = c("source", "fill_ave", "fill_zero"),
-    limit = -1,
-    offset = 0,
-    versions_before = NULL,
-    geo_value = NULL,
-    time_value = NULL) {
-  source <- rlang::arg_match(source)
+    version_query = NULL) {
+  source <- rlang::arg_match(source, values = c("nssp", "nhsn"))
+  stopifnot(is.character(signal), length(signal) == 1L)
+  geo_type <- rlang::arg_match(geo_type, values = c("state", "nation"))
   fill_method <- rlang::arg_match(fill_method)
-  geo_type <- rlang::arg_match(geo_type)
   columns <- columns %||% c("geo_value", "time_value", "value")
 
   httr2::request("https://delphi.cmu.edu/cast-api/epidata/v2") %>%
     httr2::req_url_query(
       source = source,
       signal = signal,
       geo_type = geo_type,
-      versions_before = versions_before,
+      versions_before = version_query,
       columns = columns,
-      limit = limit,
-      offset = offset,
       fill_method = fill_method,
-      geo_value = geo_value,
-      time_value = time_value,
       .multi = "explode"
     )
 }

scripts/covid_hosp_prod.R

@@ -201,12 +201,12 @@ parameters_and_date_targets <- rlang::list2(
     name = covid_data_substitutions,
     command = "scripts/covid_data_substitutions.csv"
   ),
-  tar_target(
+  tar_change(
     name = nhsn_archive_data,
+    change = get_cast_api_latest_update_date(source = "nhsn"),
     command = {
       get_nhsn_data_archive("covid")
-    },
-    cue = tar_cue("always")
+    }
   ),
   tar_target(
     name = nhsn_latest_data,
@@ -216,12 +216,12 @@ parameters_and_date_targets <- rlang::list2(
         filter(geo_value %nin% g_insufficient_data_geos)
     }
   ),
-  tar_target(
+  tar_change(
     name = nssp_archive_data,
+    change = get_cast_api_latest_update_date(source = "nssp"),
     command = {
       up_to_date_nssp_state_archive("covid")
-    },
-    cue = tar_cue("always")
+    }
   ),
   tar_target(
     name = nssp_latest_data,

scripts/flu_hosp_prod.R

@@ -242,12 +242,12 @@ parameters_and_date_targets <- rlang::list2(
         filter(source != "nhsn")
     }
   ),
-  tar_target(
+  tar_change(
     name = nhsn_archive_data,
+    change = get_cast_api_latest_update_date(source = "nhsn"),
     command = {
       get_nhsn_data_archive("flu")
-    },
-    cue = tar_cue("always")
+    }
   ),
   tar_target(
     name = nhsn_latest_data,
@@ -257,15 +257,12 @@ parameters_and_date_targets <- rlang::list2(
         filter(geo_value %nin% g_insufficient_data_geos)
     }
   ),
-  # TODO: Currently metadata queries are slow 25s, while downloading takes 0.5s. Optimize later.
-  # tar_change(
-  # change = get_cast_api_latest_update_date(source = "nssp"),
-  tar_target(
+  tar_change(
     name = nssp_archive_data,
+    change = get_cast_api_latest_update_date(source = "nssp"),
     command = {
       up_to_date_nssp_state_archive("influenza")
-    },
-    cue = tar_cue("always")
+    }
   ),
   tar_target(
     name = nssp_latest_data,