okay;

build_report.sh

@@ -12,7 +12,10 @@ for arg in "$@"; do
         --report_date=*)
             report_date="${arg#*=}"
             ;;
-        *)
+        --data_dir=*)
+                   data_dir="${arg#*=}"
+                   ;;
+               *)
             echo "Unknown option: $arg"
             exit 1
             ;;
@@ -20,8 +23,8 @@ for arg in "$@"; do
 done
 
 # Check if required arguments are set
-if [ -z "$filename" ] || [ -z "$weeks_ago" ] || [ -z "$report_date" ]; then
+if [ -z "$filename" ] || [ -z "$weeks_ago" ] || [ -z "$report_date" ] || [ -z "$data_dir" ]; then
-    echo "Missing arguments. Use: build_reports.sh --filename=hello.txt --weeks_ago=3 --report_date=2020-01-01"
+    echo "Missing arguments. Use: build_reports.sh --filename=hello.txt --weeks_ago=3 --report_date=2020-01-01 --data_dir=chemba"
     exit 1
 fi
 
@@ -29,6 +32,7 @@ fi
 echo "Filename: $filename"
 echo "Weeks ago: $weeks_ago"
 echo "Report date: $report_date"
+echo "Data directory: $data_dir"
 
 if [ "$(uname)" == "Darwin" ]; then
     # Commando's voor Mac
@@ -40,4 +44,4 @@ elif [ "$(uname)" == "Linux" ]; then
 else
     echo "Onbekend systeem"
 fi
-Rscript -e "rmarkdown::render('CI_report_dashboard_planet.Rmd', output_file='$filename', params=list(ref='$ref', report_date='$report_date'))"
+Rscript -e "rmarkdown::render('CI_report_dashboard_planet.Rmd', output_file='$filename', params=list(ref='$ref', report_date='$report_date', data_dir='$data_dir'))"

r_app/2_CI_data_prep.R

@@ -37,14 +37,15 @@ if (!is.character(project_dir)) {
   project_dir <- "chemba"
 }
 
-laravel_storage_dir <- here("../laravel_app/storage/app", project_dir)
+
+laravel_storage_dir <- here("laravel_app/storage/app", project_dir)
 #preparing directories
 planet_tif_folder <- here(laravel_storage_dir, "merged_tif")
 merged_final <- here(laravel_storage_dir, "merged_final_tif")
 
-new_project_question = TRUE
+new_project_question = FALSE
-planet_tif_folder <- here(laravel_storage_dir, project, "merged_tif")
+planet_tif_folder <- here(laravel_storage_dir, "merged_tif")
-merged_final <- here(laravel_storage_dir, project,"merged_final_tif")
+merged_final <- here(laravel_storage_dir, "merged_final_tif")
 
 data_dir <- here(laravel_storage_dir, "Data")
 extracted_CI_dir <- here(data_dir, "extracted_ci")
@@ -54,7 +55,6 @@ cumulative_CI_vals_dir <- here(extracted_CI_dir, "cumulative_vals")
 weekly_CI_mosaic <- here(laravel_storage_dir, "weekly_mosaic")
 daily_vrt <- here(data_dir, "vrt")
 harvest_dir <-  here(data_dir, "HarvestData")
-
 dir.create(here(data_dir))
 dir.create(here(extracted_CI_dir))
 dir.create(here(daily_CI_vals_dir))
@@ -66,12 +66,11 @@ dir.create(harvest_dir)
 
 
 
-
 # Creating weekly mosaic
 dates <- date_list(weeks_ago)
 
 #load pivot geojson
-pivot_sf_q <- st_read(here( "pivot_20210625.geojson")) %>% dplyr::select(pivot, pivot_quadrant) %>% vect()
+pivot_sf_q <- st_read(here(data_dir, "pivot.geojson")) %>% dplyr::select(pivot, pivot_quadrant) %>% vect()
 
 raster_files <- list.files(planet_tif_folder,full.names = T, pattern = ".tif")
 head(raster_files)
@@ -266,7 +265,7 @@ extract_rasters_daily <- function(file, field_geojson, quadrants = TRUE, save_di
 }
 
 # pivot_sf_q <- st_read(here("..", "Data", "pivot_20210625.geojson")) %>% dplyr::select(pivot, pivot_quadrant) %>% vect()
-pivot_sf <- st_read(here(data_dir, "pivot_20210625.geojson")) %>% dplyr::select(pivot, pivot_quadrant)   %>% group_by(pivot) %>% summarise() %>% vect()
+pivot_sf <- st_read(here(data_dir, "pivot.geojson")) %>% dplyr::select(pivot, pivot_quadrant)   %>% group_by(pivot) %>% summarise() %>% vect()
 message("pivot loaded")
 
 raster_files_NEW <- list.files(merged_final,full.names = T, pattern = ".tif")

r_app/CI_report_dashboard_planet.Rmd

@@ -4,6 +4,7 @@ params:
   ref: word-styles-reference-var1.docx
   output_file: "CI_report.docx"
   report_date: "2023-12-12"
+  data_dir: "chemba"
 output:
   word_document:
     reference_docx: !expr file.path("word-styles-reference-var1.docx")
@@ -45,12 +46,13 @@ library(CAST)
 ```
 
 ```{r directories, message=FALSE, warning=FALSE, include=FALSE}
-laravel_storage_dir <- here("../laravel_app/storage/app/chemba")
+laravel_storage_dir <- here("laravel_app/storage/app/",params$data_dir)
-data_dir <- here(laravel_storage_dir, "../Data")
+
-extracted_CI_dir <- here(data_dir, "extracted_ci")
+data_dir_project <- here(laravel_storage_dir, "Data")
+extracted_CI_dir <- here(data_dir_project, "extracted_ci")
 daily_CI_vals_dir <- here(extracted_CI_dir, "daily_vals")
 cumulative_CI_vals_dir <- here(extracted_CI_dir, "cumulative_vals")
-harvest_dir <-  here(data_dir, "HarvestData")
+harvest_dir <-  here(data_dir_project, "HarvestData")
 
 weekly_CI_mosaic <- here(laravel_storage_dir, "weekly_mosaic")
 
@@ -116,11 +118,11 @@ CI_m3 <- brick(here(weekly_CI_mosaic, paste0("week_",week_minus_3, "_", year_3,
 last_week_dif_raster_abs <- (CI - CI_m1)
 three_week_dif_raster_abs <- (CI - CI_m3)
 
-AllPivots0 <-st_read(here(data_dir, "pivot_20210625.geojson"))
+AllPivots0 <-st_read(here(data_dir_project, "pivot.geojson"))
 AllPivots0$pivot  <- factor(AllPivots0$pivot, levels = c("1.1", "1.2", "1.3", "1.4", "1.6", "1.7", "1.8", "1.9", "1.10", "1.11", "1.12", "1.13", "1.14" , "1.16" , "1.17" , "1.18" ,"2.1", "2.2", "2.3" , "2.4", "2.5", "3.1", "3.2", "3.3", "4.1", "4.2", "4.3", "4.4", "4.5", "4.6", "5.1" ,"5.2", "5.3", "5.4", "6.1", "6.2", "DL1.1", "DL1.3"))
 
 
-joined_spans <-st_read(here(data_dir, "spans2.geojson")) %>% st_transform(crs(AllPivots0))
+joined_spans <-st_read(here(data_dir_project, "span.geojson")) %>% st_transform(crs(AllPivots0))
 
 pivots_dates <- readRDS(here(harvest_dir, "harvest_data_new")) %>% filter(
   pivot %in% c("1.1", "1.2", "1.3", "1.4",  "1.7", "1.8", "1.9", "1.10", "1.11", "1.12", "1.13",