Merge pull request #68 from HopkinsIDD/configwriter_fix

Configwriter fix
HopkinsIDD · Oct 6, 2023 · 8a84db7 · 8a84db7
2 parents f065d3d + 4cc949a
commit 8a84db7
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Showing 2 changed files with 14 additions and 10 deletions.
diff --git a/datasetup/build_covid_data.R b/datasetup/build_covid_data.R
@@ -49,12 +49,12 @@ source(file.path(opt$path, "datasetup/data_setup_source.R"))
 # SET DELPHI API KEY ------------------------------------------------------
 
 if (any(grepl("nchs|hhs", opt$gt_data_source))){
-    if (!is.null(opt$delphi_api_key)){
-        cat(paste0("Using Environment variable for Delphi API key: ", opt$delphi_api_key))
-        options(covidcast.auth = opt$delphi_api_key)
-    } else if (!is.null(config$inference$gt_api_key)){
+    if (!is.null(config$inference$gt_api_key)){
         cat(paste0("Using Config variable for Delphi API key: ", config$inference$gt_api_key))
         options(covidcast.auth = config$inference$gt_api_key)
+    } else if (!is.null(opt$delphi_api_key)){
+        cat(paste0("Using Environment variable for Delphi API key: ", opt$delphi_api_key))
+        options(covidcast.auth = opt$delphi_api_key)
     } else {
         newkey <- readline(prompt = "Please enter your Delphi API key before proceeding:")
         #check

diff --git a/flepimop/R_packages/config.writer/R/yaml_utils.R b/flepimop/R_packages/config.writer/R/yaml_utils.R
@@ -1976,15 +1976,19 @@ seir_chunk <- function(resume_modifier = NULL,
                    "      proportion_exponent: [\n",
                    "        [",rate_propexp_parts, ",\"1\",\"1\",\"1\"],\n",
                    "        [",rate_alpha_parts, ",\"1\",\"1\",\"1\"]]\n",
-                   "      rate: [\n",
-                   paste0(sapply(X = na.omit(c(rate_seir_parts, rate_vacc_parts, rate_var_parts, rate_age_parts)),
-                              function(x = X){ paste0("        ",x,",\n")}) ),
-                   "      ]\n"),
+                   "      rate: [",
+                   ifelse(nchar(rate_seir_parts)<100,
+                          paste(na.omit(c(rate_seir_parts, rate_vacc_parts, rate_var_parts, rate_age_parts)), collapse = ", "),
+                          paste0("\n        ", paste(na.omit(c(rate_seir_parts, rate_vacc_parts, rate_var_parts, rate_age_parts)), collapse = ",\n        "))),
+                   "]\n"),
                paste0(
                    "      proportional_to: [\"source\"]\n",
                    "      proportion_exponent: [[\"1\",\"1\",\"1\",\"1\"]]\n",
-                   "      rate: [", paste(na.omit(c(rate_seir_parts, rate_vacc_parts, rate_var_parts, rate_age_parts)), collapse = ", "), "]\n")),
-                   # "      rate: [", glue::glue_collapse(na.omit(c(rate_seir_parts, rate_vacc_parts, rate_var_parts, rate_age_parts)), collapse = ", "), "]\n")),
+                   "      rate: [",
+                   ifelse(nchar(rate_seir_parts)<100,
+                          paste(na.omit(c(rate_seir_parts, rate_vacc_parts, rate_var_parts, rate_age_parts)), collapse = ", "),
+                          paste0("\n        ", paste(na.omit(c(rate_seir_parts, rate_vacc_parts, rate_var_parts, rate_age_parts)), collapse = ",\n        "))),
+                   "]\n")),
         "\n")
 
     return(tmp)