pathing and other tweaks for Docker

workspace/05_hyRefactor_flines.Rmd

@@ -23,7 +23,6 @@ knitr::opts_chunk$set(
 Load functions and configuration. 
 See `hyRefactory_config.R` for all constants.
 ```{r setup}
-source("../hyfabric/R/utils.R")
 source("R/utils.R")
 source("R/hyRefactor_funs.R")
 source("R/config.R")

workspace/07-2_aggregate_cats.Rmd

@@ -20,7 +20,6 @@ knitr::opts_chunk$set(
 Load functions and configuration. 
 See `hyRefactory_config.R` for all constants.
 ```{r setup}
-source("../hyfabric/R/utils.R")
 source("R/utils.R")
 source("R/config.R")
 source("R/NHD_navigate.R")
@@ -71,7 +70,7 @@ if(needs_layer(out_agg_gpkg, mapped_outlets_layer)) {
     # Map non-event outlets ID into one dataset here with reconciled ID 
     outlets_POI <- map_outlet_ids(select(st_drop_geometry(outlets), COMID, type), 
                                      reconciled_sub) %>%
-      left_join(mutate(outlets, COMID = as.character(COMID)) %>% select(-type), by = "COMID") %>%
+      left_join(outlets %>% select(-type), by = "COMID") %>%
       st_sf()
   
     # Get the end of the reconciled flowlines and bind with data frame

workspace/R/config.R

@@ -15,10 +15,10 @@ if(!exists("VPU")) {
   VPU <- get_rpu_dependent_vars(rpu_code)$v
 }
 
-if(!nchar(out_gpkg <- Sys.getenv("OUT_GPKG")) > 5) 
+if(!nchar(out_agg_gpkg <- Sys.getenv("OUT_GPKG")) > 5) 
   out_agg_gpkg <- file.path("cache", paste0(rpu_code, "_aggregate.gpkg"))
 
-if(!nchar(out_refactor_gpkg <- Sys.getenv("OUT_REFACTOR_GPKG")) > 5)
+if(!nchar(out_refac_gpkg <- Sys.getenv("OUT_REFACTOR_GPKG")) > 5)
   out_refac_gpkg <- file.path("cache", paste0(rpu_code, "_refactor.gpkg"))
 
 if(!nchar(cache_split <- Sys.getenv("CACHE_SPLIT")) > 5) 

workspace/runners/make_docker_calls.Rmd

@@ -23,7 +23,10 @@ e1 <- "--env HYDREG=z!z"
 
 command <- paste("R -e \"rmarkdown::render('/jupyter/02_NHD_navigate.Rmd', output_file='/jupyter/reports/02_NHD_navigate_z!z.html')\" \n")
 
-hus <- c(paste0("0", c(1:9)), paste0("1", c(1:8)), "10U", "10L")
+hus <- c(paste0("0", c(1:2, 4:9)), 
+         "03S", "03W", "03L",
+         "10U", "10L",
+         paste0("1", c(1:8)))
 
 calls <- sapply(hus, function(hu) gsub("z!z", hu, paste(call, mount, e1, docker_image, command)))
 
@@ -73,13 +76,15 @@ The txt file can be used with GNU parallel like:
 ```{r}
 out_script <- "hyRefactor_calls.txt"
 
-e1 <- "--env OUT_GPKG=/jupyter/cache/z!z.gpkg"
+e1 <- "--env OUT_GPKG=/jupyter/cache/z!z_aggregate.gpkg"
+e11 <- "--env OUT_REFACTOR_GPKG=/jupyter/cache/z!z_refactor.gpkg"
 e2 <- "--env RPU_CODE=z!z"
 e3 <- "--env SPLIT_CACHE=/jupyter/temp/z!z_split.rda"
 e4 <- "--env LOOKUP_TABLE=/jupyter/cache/z!z_lookup.csv"
 
 command <- paste("R -e \"rmarkdown::render('/jupyter/05_hyRefactor_flines.Rmd', output_file='/jupyter/reports/05_hyRefactor_flines_z!z.html')\"",
-                 "-e \"rmarkdown::render('/jupyter/07_hyRefactor_cats.Rmd', output_file='/jupyter/reports/07_hyRefactor_cats_z!z.html')\" \n")
+                 "-e \"rmarkdown::render('/jupyter/07-1_hyRefactor_cats.Rmd', output_file='/jupyter/reports/07-1_hyRefactor_cats_z!z.html')\"",
+                 "-e \"rmarkdown::render('/jupyter/07-2_aggregate_cats.Rmd', output_file='/jupyter/reports/07-2_aggregate_cats_z!z.html')\" \n")
 
 all_hus <- gsub("rpu_", "", names(data_paths$fdr))
 
@@ -88,7 +93,7 @@ errors <- gsub(".rda", "", gsub("temp/", "", errors))
 
 hus <- all_hus[!all_hus %in% errors]
 
-calls <- sapply(hus, function(hu) gsub("z!z", hu, paste(call, mount, e1, e2, e3, e4, docker_image, command)))
+calls <- sapply(hus, function(hu) gsub("z!z", hu, paste(call, mount, e1, e11, e2, e3, e4, docker_image, command)))
 
 cat("", file = out_script, append = FALSE)
 for(i in 1:length(calls)) {