[USGS-R#27] variable target output location

jsadler2 · Dec 14, 2021 · eb488e4 · eb488e4
1 parent dee3ace
commit eb488e4
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Showing 4 changed files with 25 additions and 20 deletions.
diff --git a/1_fetch.R b/1_fetch.R
@@ -15,7 +15,7 @@ p1_targets_list <- list(
   # Load harmonized WQP data product for discrete samples
   tar_target(
     p1_wqp_data,
-    fetch_harmonized_wqp_data("1_fetch/out")),
+    fetch_harmonized_wqp_data(file.path(run_dir, "1_fetch/out"))),
 
   # Identify NWIS sites with DO data 
   tar_target(
@@ -41,7 +41,7 @@ p1_targets_list <- list(
 
   tar_target(
     p1_daily_data_csv,
-    write_to_csv(p1_daily_data, outfile="1_fetch/out/daily_do_data.csv"),
+    write_to_csv(p1_daily_data, outfile=file.path(run_dir, "1_fetch/out/daily_do_data.csv")),
     format = "file"),
 
   # Subset NWIS sites with sub-daily data
@@ -59,7 +59,7 @@ p1_targets_list <- list(
 
   tar_target(
     p1_inst_data_csv,
-    write_to_csv(p1_inst_data, outfile="1_fetch/out/inst_do_data.csv"),
+    write_to_csv(p1_inst_data, outfile=file.path(run_dir, "1_fetch/out/inst_do_data.csv")),
     format = "file"
   ),
 
@@ -77,7 +77,7 @@ p1_targets_list <- list(
 
   tar_target(
     p1_reaches_shp_unzipped,
-    {shapedir = "1_fetch/out/study_stream_reaches"
+    {shapedir = file.path(run_dir, "1_fetch/out/study_stream_reaches")
     unzip(p1_reaches_shp_zip, exdir = shapedir)},
     format = "file"
   ),
@@ -90,7 +90,7 @@ p1_targets_list <- list(
   # fetch prms met data
   tar_target(
     p1_prms_met_data_zip_file,
-    fetch_prms_met_data("1_fetch/out", "sntemp_inputs_outputs_drb.zip"),
+    fetch_prms_met_data(file.path(run_dir, "1_fetch/out"), "sntemp_inputs_outputs_drb.zip"),
     format = "file"),
 
   # unzip prms met data

diff --git a/2_process.R b/2_process.R
@@ -45,7 +45,7 @@ p2_targets_list <- list(
 
   tar_target(
     p2_sites_w_segs_csv,
-    write_to_csv(p2_sites_w_segs, "2_process/out/site_w_seg_ids.csv")
+    write_to_csv(p2_sites_w_segs, file.path(run_dir, "2_process/out/site_w_seg_ids.csv"))
   ),
 
   tar_target(
@@ -58,7 +58,7 @@ p2_targets_list <- list(
 
   tar_target(
     p2_daily_with_seg_ids_csv,
-    write_to_csv(p2_daily_with_seg_ids, "2_process/out/daily_do_data.csv"),
+    write_to_csv(p2_daily_with_seg_ids, file.path(run_dir, "2_process/out/daily_do_data.csv")),
     format = "file"
   ) 
 

diff --git a/3_visualize.R b/3_visualize.R
@@ -6,18 +6,18 @@ p3_targets_list <- list(
 
   # Plot daily data
   tar_target(p3_daily_timeseries_png,
-             plot_daily_data(sprintf("3_visualize/out/daily_timeseries_png/daily_data_%s.png",unique(p1_daily_data$site_no)),p1_daily_data),
+             plot_daily_data(file.path(run_dir, sprintf("3_visualize/out/daily_timeseries_png/daily_data_%s.png",unique(p1_daily_data$site_no))),p1_daily_data),
              format = "file",
              pattern = map(p1_daily_data)),
 
   # Plot instantaneous data (hourly averages)
   tar_target(p3_hourly_timeseries_png,
-             plot_inst_data(sprintf("3_visualize/out/hourly_timeseries_png/hourly_data_%s.png",unique(p2_inst_data_hourly$site_no)),p2_inst_data_hourly),
+             plot_inst_data(file.path(run_dir, sprintf("3_visualize/out/hourly_timeseries_png/hourly_data_%s.png",unique(p2_inst_data_hourly$site_no))),p2_inst_data_hourly),
              format = "file",
              pattern = map(p2_inst_data_hourly)),
 
   # Render data summary report (report target has format = "file")
-  tarchetypes::tar_render(p3_wqp_spC_report, "3_visualize/src/report-do-inventory.Rmd",output_dir = "3_visualize/out"),
+  tarchetypes::tar_render(p3_wqp_spC_report, "3_visualize/src/report-do-inventory.Rmd",output_dir = file.path(run_dir, "3_visualize/out")),
 
   tar_target(p3_do_plot_python_file,
              "3_visualize/src/do_overview_plots.py",
@@ -28,11 +28,11 @@ p3_targets_list <- list(
     plot_do_overview(p3_do_plot_python_file,
                      p1_daily_data_csv,
                      p1_inst_data_csv,
-                     filesout=c("3_visualize/out/inst_daily_means.jpg",
-                                "3_visualize/out/daily_daily_means.jpg",
-                                "3_visualize/out/doy_means.jpg",
-                                "3_visualize/out/filtered_daily_means.jpg",
-                                "3_visualize/out/filtered_inst_means.jpg")),
+                     filesout=c(file.path(run_dir, "3_visualize/out/inst_daily_means.jpg"),
+                                file.path(run_dir, "3_visualize/out/daily_daily_means.jpg"),
+                                file.path(run_dir, "3_visualize/out/doy_means.jpg"),
+                                file.path(run_dir,  "3_visualize/out/filtered_daily_means.jpg"),
+                                file.path(run_dir, "3_visualize/out/filtered_inst_means.jpg"))),
     format = "file"
   )
 )

diff --git a/_targets.R b/_targets.R
@@ -7,11 +7,16 @@ source("1_fetch.R")
 source("2_process.R")
 source("3_visualize.R")
 
-dir.create("1_fetch/out/", showWarnings = FALSE)
-dir.create("2_process/out/", showWarnings = FALSE)
-dir.create("3_visualize/out/", showWarnings = FALSE)
-dir.create("3_visualize/out/daily_timeseries_png/",showWarnings = FALSE)
-dir.create("3_visualize/out/hourly_timeseries_png/",showWarnings = FALSE)
+run_dir <- targets::tar_config_get("store")
+if (run_dir == "_targets"){
+    run_dir <- getwd()
+}
+
+dir.create(file.path(run_dir, "1_fetch/out/"), showWarnings = FALSE)
+dir.create(file.path(run_dir, "2_process/out/"), showWarnings = FALSE)
+dir.create(file.path(run_dir, "3_visualize/out/"), showWarnings = FALSE)
+dir.create(file.path(run_dir, "3_visualize/out/daily_timeseries_png/"),showWarnings = FALSE)
+dir.create(file.path(run_dir, "3_visualize/out/hourly_timeseries_png/"),showWarnings = FALSE)
 
 # Define columns of interest from harmonized WQP data
 wqp_vars_select <- c("MonitoringLocationIdentifier","MonitoringLocationName","LongitudeMeasure","LatitudeMeasure",