hotfix: few bugs caught in mentat testing

Author: dshemetov

Makefile

@@ -13,11 +13,11 @@ run:
 	Rscript scripts/run.R
 
 prod-covid:
-	export TAR_PROJECT=covid_hosp_prod; \
+	export TAR_RUN_PROJECT=covid_hosp_prod; \
 	Rscript scripts/run.R
 
 prod-flu:
-	export TAR_PROJECT=flu_hosp_prod; \
+	export TAR_RUN_PROJECT=flu_hosp_prod; \
 	Rscript scripts/run.R
 
 prod: prod-covid prod-flu update_site netlify

scripts/covid_hosp_prod.R

@@ -365,7 +365,7 @@ ensemble_targets <- tar_map(
         mutate(source = "nhsn as_of forecast") %>%
         bind_rows(nhsn_latest_data %>% mutate(source = "nhsn")) %>%
         select(geo_value, target_end_date = time_value, value) %>%
-        filter(target_end_date > truth_data_date, geo_value %nin% insufficient_data_geos)
+        filter(target_end_date > g_truth_data_date, geo_value %nin% g_insufficient_data_geos)
       nssp_data <- nssp_latest_data %>%
         select(geo_value, target_end_date = time_value, value = nssp) %>%
         filter(target_end_date > g_truth_data_date, geo_value %nin% g_insufficient_data_geos) %>%

scripts/flu_hosp_prod.R

@@ -95,7 +95,7 @@ g_windowed_seasonal_extra_sources = function(epi_data, ahead, extra_data, ...) {
         drop_non_seasons = TRUE,
         pop_scaling = FALSE,
         lags = list(c(0, 7), c(0, 7)),
-        keys_to_ignore = very_latent_locations
+        keys_to_ignore = g_very_latent_locations
       ) %>%
       select(-source) %>%
       mutate(target_end_date = target_end_date + 3) %>%

scripts/get_forecast_data.r

@@ -129,8 +129,8 @@ fetch_forecast_files <- function(sync_to_s3 = TRUE, disease) {
     for (filename in filenames) {
       pb_files$tick(tokens = list(filename = filename))
 
-      if (check_github_file(forecaster, filename)) {
-        forecast_data <- download_forecast_file(forecaster, filename)
+      if (check_github_file(forecaster, filename, disease)) {
+        forecast_data <- download_forecast_file(forecaster, filename, disease)
         if (!is.null(forecast_data)) {
           all_forecasts[[length(all_forecasts) + 1]] <- forecast_data
         }

scripts/run.R

@@ -26,9 +26,16 @@ suppressPackageStartupMessages(source(here::here("R", "load_all.R")))
 #   )
 #   # Save to disk
 #   saveRDS(scorecards, "exploration-scorecards-2023-10-04.RDS")
-tar_project <- Sys.getenv("TAR_PROJECT", "flu_hosp_prod")
+
+# This is TAR_RUN_PROJECT and not TAR_PROJECT, because the latter gets
+# overwritten by the environment variable of the same name in the shell that
+# runs this script.
+tar_project <- Sys.getenv("TAR_RUN_PROJECT", "flu_hosp_prod")
+# Where to place files in S3 (mostly unused)
 aws_s3_prefix <- Sys.getenv("AWS_S3_PREFIX", "exploration") %>% paste0("/", tar_project)
+# Where to place flu forecasts
 flu_submission_directory <- Sys.getenv("FLU_SUBMISSION_DIRECTORY", "cache")
+# Where to place covid forecasts
 covid_submission_directory <- Sys.getenv("COVID_SUBMISSION_DIRECTORY", "cache")
 cli::cli_inform(
   c(
@@ -41,7 +48,7 @@ cli::cli_inform(
 )
 
 
-# targets needs the output dir to already exist.
+# Targets needs the output dir to already exist.
 store_dir <- tar_path_store()
 if (!dir.exists(store_dir)) dir.create(store_dir)
 
@@ -70,6 +77,5 @@ restart_loop <- function() {
 
 tar_make(
   store = tar_config_get("store", project = tar_project),
-  script = tar_config_get("script", project = tar_project),
-  use_crew = TRUE
+  script = tar_config_get("script", project = tar_project)
 )