642 lines
28 KiB
R
642 lines
28 KiB
R
# ==============================================================================
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# FULL PIPELINE RUNNER
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# ==============================================================================
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# Mixed Python/R pipeline:
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# 1. Python: Download Planet images
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# 2. R 10: Create master grid and split TIFFs
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# 3. R 20: CI Extraction
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# 4. R 30: Interpolate growth model
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# 5. R 21: Convert CI RDS to CSV (uses Script 30 output)
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# 6. Python 31: Harvest imminent weekly
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# 7. R 40: Mosaic creation
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# 8. R 80: Calculate KPIs
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# 9. R 90 (Agronomic) OR R 91 (Cane Supply): Generate Word Report
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#
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# ==============================================================================
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# HOW TO RUN THIS SCRIPT
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# ==============================================================================
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#
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# Run from the smartcane/ directory:
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#
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# Option 1 (Recommended - shows real-time output):
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# Rscript r_app/run_full_pipeline.R
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#
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# Option 2 (Full path to Rscript - use & in PowerShell for paths with spaces):
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# & "C:\Program Files\R\R-4.4.3\bin\x64\Rscript.exe" r_app/run_full_pipeline.R
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#
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# Option 3 (Batch mode - output saved to .Rout file):
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# R CMD BATCH --vanilla r_app/run_full_pipeline.R
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#
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# ==============================================================================
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# ==============================================================================
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# *** EDIT THESE VARIABLES ***
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end_date <- as.Date("2026-02-04") # or specify: as.Date("2026-01-27") , Sys.Date()
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offset <- 7 # days to look back
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project_dir <- "angata" # project name: "esa", "aura", "angata", "chemba"
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force_rerun <- FALSE # Set to TRUE to force all scripts to run even if outputs exist
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migrate_legacy_format <- TRUE # Set to TRUE to migrate from old format (merged_tif/merged_tif_8b) to new format (field_tiles)
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# *** NOTE: data_source is now unified - all projects use field_tiles after migration ***
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# ***************************
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# Format dates
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end_date_str <- format(as.Date(end_date), "%Y-%m-%d")
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# Track success of pipeline
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pipeline_success <- TRUE
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# ==============================================================================
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# INTELLIGENT CHECKING: What has already been completed?
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# ==============================================================================
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cat("\n========== CHECKING EXISTING OUTPUTS ==========\n")
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# Check Script 10 outputs (field_tiles with per-field TIFFs)
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# Script 10 outputs to field_tiles/{field_id}/{date}.tif
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field_tiles_dir <- file.path("laravel_app", "storage", "app", project_dir, "field_tiles")
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tiles_dates <- c()
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if (dir.exists(field_tiles_dir)) {
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# Get all field subdirectories
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field_dirs <- list.dirs(field_tiles_dir, full.names = TRUE, recursive = FALSE)
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if (length(field_dirs) > 0) {
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# Get unique dates from all field directories
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all_files <- list.files(field_dirs, pattern = "^\\d{4}-\\d{2}-\\d{2}\\.tif$")
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tiles_dates <- unique(sub("\\.tif$", "", all_files))
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}
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}
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cat(sprintf("Script 10: %d dates already tiled (field_tiles/)\n", length(tiles_dates)))
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# Check Script 20 outputs (CI extraction) - per-field CI TIFFs at field_tiles_CI/{FIELD}/{DATE}.tif
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# NOTE: This is the NEW per-field format, not the old extracted_ci/ flat format
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field_tiles_ci_dir <- file.path("laravel_app", "storage", "app", project_dir, "field_tiles_CI")
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ci_tiff_dates <- c()
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if (dir.exists(field_tiles_ci_dir)) {
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# Get all field subdirectories
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field_dirs <- list.dirs(field_tiles_ci_dir, full.names = TRUE, recursive = FALSE)
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if (length(field_dirs) > 0) {
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# Get unique dates from all field directories (dates that have been processed through Script 20)
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all_files <- list.files(field_dirs, pattern = "^\\d{4}-\\d{2}-\\d{2}\\.tif$")
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ci_tiff_dates <- unique(sub("\\.tif$", "", all_files))
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}
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}
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cat(sprintf("Script 20: %d dates already processed (field_tiles_CI/)\n", length(ci_tiff_dates)))
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# Check Script 21 outputs (CSV conversion) - note: this gets overwritten each time, so we don't skip based on this
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# Instead, check if CI RDS files exist - if they do, 21 should also run
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# For now, just note that CSV is time-dependent, not a good skip indicator
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cat("Script 21: CSV file exists but gets overwritten - will run if Script 20 runs\n")
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# Check Script 40 outputs (mosaics in weekly_tile_max/5x5)
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mosaic_dir <- file.path("laravel_app", "storage", "app", project_dir, "weekly_tile_max")
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mosaic_files <- if (dir.exists(mosaic_dir)) {
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list.files(mosaic_dir, pattern = "\\.tif$")
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} else {
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c()
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}
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cat(sprintf("Script 40: %d mosaic files exist\n", length(mosaic_files)))
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# Check Script 80 outputs (KPIs in reports/kpis/field_stats)
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kpi_dir <- file.path("laravel_app", "storage", "app", project_dir, "reports", "kpis", "field_stats")
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kpi_files <- if (dir.exists(kpi_dir)) {
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list.files(kpi_dir, pattern = "\\.csv$|\\.json$")
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} else {
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c()
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}
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cat(sprintf("Script 80: %d KPI files exist\n", length(kpi_files)))
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# Determine if scripts should run based on outputs
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skip_10 <- FALSE # Script 10 should always run to pick up any new merged_tif files
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skip_20 <- FALSE # Script 20 always runs to process dates in the current window (per-field format)
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skip_21 <- FALSE # Skip 21 only if 20 is skipped
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skip_40 <- length(mosaic_files) > 0 && !force_rerun
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skip_80 <- FALSE # Always run Script 80 - it calculates KPIs for the current week (end_date), not historical weeks
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cat("\nSkipping decisions:\n")
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cat(sprintf(" Script 10: %s\n", if(skip_10) "SKIP (tiles exist)" else "RUN"))
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cat(sprintf(" Script 20: %s\n", if(skip_20) "SKIP (CI exists)" else "RUN"))
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cat(sprintf(" Script 21: %s\n", if(skip_21) "SKIP (CI exists)" else "RUN"))
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cat(sprintf(" Script 40: %s\n", if(skip_40) "SKIP (mosaics exist)" else "RUN"))
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cat(sprintf(" Script 80: %s\n", if(skip_80) "SKIP (KPIs exist)" else "RUN"))
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# ==============================================================================
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# PYTHON: DOWNLOAD PLANET IMAGES (MISSING DATES ONLY)
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# ==============================================================================
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cat("\n========== DOWNLOADING PLANET IMAGES (MISSING DATES ONLY) ==========\n")
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tryCatch({
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# Setup paths
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base_path <- file.path("laravel_app", "storage", "app", project_dir)
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# Always check merged_tif/ for existing downloads (both modes)
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# merged_tif/ is where Python downloads go, before Script 10 splits to field_tiles/
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merged_tifs_dir <- file.path(base_path, "merged_tif")
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existing_tiff_files <- list.files(merged_tifs_dir, pattern = "^\\d{4}-\\d{2}-\\d{2}\\.tif$")
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existing_tiff_dates <- sub("\\.tif$", "", existing_tiff_files)
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if (migrate_legacy_format) {
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cat(sprintf(" Migration mode: Checking merged_tif/ for existing dates\n"))
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} else {
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cat(sprintf(" Production mode: Checking merged_tif/ and field_tiles/ for existing dates\n"))
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}
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# Find missing dates in the window
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# Window: from (end_date - offset) to end_date
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# Example: if end_date=2026-02-04 and offset=7, window is 2026-01-28 to 2026-02-04 (8 dates)
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start_date <- end_date - offset
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date_seq <- seq(start_date, end_date, by = "day")
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target_dates <- format(date_seq, "%Y-%m-%d")
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# Also check field_tiles/ for dates that have already been processed through Script 10
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# field_tiles/ contains {field_id}/{date}.tif files - check which dates are present
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field_tiles_dir <- file.path(base_path, "field_tiles")
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processed_dates <- c()
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if (dir.exists(field_tiles_dir)) {
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# Get all field subdirectories
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field_dirs <- list.dirs(field_tiles_dir, full.names = TRUE, recursive = FALSE)
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if (length(field_dirs) > 0) {
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# Get unique dates from all field directories
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all_files <- list.files(field_dirs, pattern = "^\\d{4}-\\d{2}-\\d{2}\\.tif$")
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processed_dates <- unique(sub("\\.tif$", "", all_files))
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}
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}
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# Combine existing dates from both merged_tif and field_tiles
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all_existing_dates <- unique(c(existing_tiff_dates, processed_dates))
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# Compare: which target dates don't exist in merged_tif/ or field_tiles/?
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missing_dates <- target_dates[!(target_dates %in% all_existing_dates)]
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cat(sprintf(" Existing dates in merged_tif/: %d\n", length(existing_tiff_dates)))
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cat(sprintf(" Processed dates in field_tiles/: %d\n", length(processed_dates)))
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cat(sprintf(" Target window: %s to %s (%d dates)\n", start_date, end_date, length(target_dates)))
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cat(sprintf(" Missing dates to download: %d\n", length(missing_dates)))
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# Download each missing date
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download_count <- 0
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download_failed <- 0
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if (length(missing_dates) > 0) {
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# Save current directory
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original_dir <- getwd()
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# Change to python_app directory so relative paths work correctly
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setwd("python_app")
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for (date_str in missing_dates) {
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cmd <- sprintf('python 00_download_8band_pu_optimized.py "%s" --date "%s" --resolution 3 --cleanup', project_dir, date_str)
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result <- system(cmd, ignore.stdout = FALSE, ignore.stderr = FALSE)
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if (result == 0) {
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download_count <- download_count + 1
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} else {
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download_failed <- download_failed + 1
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}
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}
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# Change back to original directory
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setwd(original_dir)
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}
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cat(sprintf("✓ Downloaded %d dates, %d failed\n", download_count, download_failed))
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if (download_failed > 0) {
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cat("⚠ Some downloads failed, but continuing pipeline\n")
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}
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# Force Script 10 to run ONLY if downloads actually succeeded (not just attempted)
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if (download_count > 0) {
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skip_10 <- FALSE
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}
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}, error = function(e) {
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cat("✗ Error in planet download:", e$message, "\n")
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pipeline_success <<- FALSE
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})
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# ==============================================================================
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# MIGRATION: Move legacy format files to new format (if enabled)
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# ==============================================================================
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if (pipeline_success && migrate_legacy_format) {
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cat("\n========== MIGRATION: MOVING LEGACY FORMAT FILES ==========\n")
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tryCatch({
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base_path <- file.path("laravel_app", "storage", "app", project_dir)
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# PART 1: Move merged_tif files to field_tiles
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merged_tif_old <- file.path(base_path, "merged_tif")
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field_tiles_new <- file.path(base_path, "field_tiles")
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if (dir.exists(merged_tif_old)) {
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tif_files <- list.files(merged_tif_old, pattern = "\\.tif$", full.names = TRUE)
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if (length(tif_files) > 0) {
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dir.create(field_tiles_new, showWarnings = FALSE, recursive = TRUE)
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for (file in tif_files) {
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file.rename(file, file.path(field_tiles_new, basename(file)))
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}
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cat(sprintf("✓ Moved %d TIFF files from merged_tif/ to field_tiles/\n", length(tif_files)))
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}
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}
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# PART 2: Move merged_tif_final files (CI) to field_tiles_CI
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merged_tif_final_old <- file.path(base_path, "merged_tif_final")
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field_tiles_ci_new <- file.path(base_path, "field_tiles_CI")
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if (dir.exists(merged_tif_final_old)) {
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ci_files <- list.files(merged_tif_final_old, pattern = "\\.tif$", full.names = TRUE)
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if (length(ci_files) > 0) {
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dir.create(field_tiles_ci_new, showWarnings = FALSE, recursive = TRUE)
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for (file in ci_files) {
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file.rename(file, file.path(field_tiles_ci_new, basename(file)))
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}
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cat(sprintf("✓ Moved %d CI TIFF files from merged_tif_final/ to field_tiles_CI/\n", length(ci_files)))
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}
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}
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cat("✓ Migration completed successfully\n")
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}, error = function(e) {
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cat("✗ Error in migration:", e$message, "\n")
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pipeline_success <<- FALSE
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})
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}
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# ==============================================================================
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# SCRIPT 10: CREATE MASTER GRID AND SPLIT TIFFs
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# ==============================================================================
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if (pipeline_success && !skip_10) {
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cat("\n========== RUNNING SCRIPT 10: CREATE MASTER GRID AND SPLIT TIFFs ==========\n")
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tryCatch({
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# Set environment variables for the script (Script 10 uses these for filtering)
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assign("PROJECT", project_dir, envir = .GlobalEnv)
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assign("end_date", end_date, envir = .GlobalEnv)
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assign("offset", offset, envir = .GlobalEnv)
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# Count field_tiles/ dates BEFORE Script 10 runs
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field_tiles_dir <- file.path("laravel_app", "storage", "app", project_dir, "field_tiles")
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field_dirs_before <- c()
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if (dir.exists(field_tiles_dir)) {
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field_dirs_tmp <- list.dirs(field_tiles_dir, full.names = TRUE, recursive = FALSE)
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if (length(field_dirs_tmp) > 0) {
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all_files_before <- list.files(field_dirs_tmp, pattern = "^\\d{4}-\\d{2}-\\d{2}\\.tif$")
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field_dirs_before <- unique(sub("\\.tif$", "", all_files_before))
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}
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}
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# Suppress verbose per-date output, show only summary
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sink(nullfile())
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source("r_app/10_create_per_field_tiffs.R")
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sink()
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# Count field_tiles/ dates AFTER Script 10 runs
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field_dirs_after <- c()
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if (dir.exists(field_tiles_dir)) {
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field_dirs_tmp <- list.dirs(field_tiles_dir, full.names = TRUE, recursive = FALSE)
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if (length(field_dirs_tmp) > 0) {
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all_files_after <- list.files(field_dirs_tmp, pattern = "^\\d{4}-\\d{2}-\\d{2}\\.tif$")
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field_dirs_after <- unique(sub("\\.tif$", "", all_files_after))
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}
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}
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# Calculate newly added dates
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newly_added <- length(field_dirs_after) - length(field_dirs_before)
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cat(sprintf("✓ Script 10 completed - processed %d new dates (total: %d dates in field_tiles/)\n", max(0, newly_added), length(field_dirs_after)))
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}, error = function(e) {
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sink()
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cat("✗ Error in Script 10:", e$message, "\n")
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pipeline_success <<- FALSE
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})
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} else if (skip_10) {
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cat("\n========== SKIPPING SCRIPT 10 (tiles already exist) ==========\n")
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}
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# ==============================================================================
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# SCRIPT 20: CI EXTRACTION
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# ==============================================================================
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if (pipeline_success && !skip_20) {
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cat("\n========== RUNNING SCRIPT 20: CI EXTRACTION ==========\n")
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tryCatch({
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# Set environment variables for the script
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assign("end_date", end_date, envir = .GlobalEnv)
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assign("offset", offset, envir = .GlobalEnv)
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assign("project_dir", project_dir, envir = .GlobalEnv)
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# If in migration mode, find all dates that need processing
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if (migrate_legacy_format) {
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cat("Migration mode: Finding all dates in field_tiles/ that need CI processing...\n")
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# Get all dates from field_tiles/
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field_tiles_dir_check <- file.path("laravel_app", "storage", "app", project_dir, "field_tiles")
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all_dates_in_tiles <- c()
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if (dir.exists(field_tiles_dir_check)) {
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field_dirs_tmp <- list.dirs(field_tiles_dir_check, full.names = TRUE, recursive = FALSE)
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if (length(field_dirs_tmp) > 0) {
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all_files_tmp <- list.files(field_dirs_tmp, pattern = "^\\d{4}-\\d{2}-\\d{2}\\.tif$")
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all_dates_in_tiles <- unique(sub("\\.tif$", "", all_files_tmp))
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}
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}
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# Get dates already processed in field_tiles_CI/
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field_tiles_ci_check <- file.path("laravel_app", "storage", "app", project_dir, "field_tiles_CI")
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processed_ci_dates <- c()
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if (dir.exists(field_tiles_ci_check)) {
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field_dirs_ci <- list.dirs(field_tiles_ci_check, full.names = TRUE, recursive = FALSE)
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if (length(field_dirs_ci) > 0) {
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all_files_ci <- list.files(field_dirs_ci, pattern = "^\\d{4}-\\d{2}-\\d{2}\\.tif$")
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processed_ci_dates <- unique(sub("\\.tif$", "", all_files_ci))
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}
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}
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# Get dates already in old RDS format
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old_rds_dir <- file.path("laravel_app", "storage", "app", project_dir, "Data", "extracted_ci", "daily_vals")
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processed_rds_dates <- c()
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if (dir.exists(old_rds_dir)) {
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rds_files <- list.files(old_rds_dir, pattern = "^\\d{4}-\\d{2}-\\d{2}\\.rds$")
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processed_rds_dates <- unique(sub("\\.rds$", "", rds_files))
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}
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# Find dates missing from either location
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dates_missing_ci <- all_dates_in_tiles[!(all_dates_in_tiles %in% processed_ci_dates)]
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dates_missing_rds <- all_dates_in_tiles[!(all_dates_in_tiles %in% processed_rds_dates)]
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dates_to_process_migration <- sort(unique(c(dates_missing_ci, dates_missing_rds)))
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cat(sprintf(" All dates in field_tiles/: %d\n", length(all_dates_in_tiles)))
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cat(sprintf(" Already in field_tiles_CI/: %d\n", length(processed_ci_dates)))
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cat(sprintf(" Already in extracted_ci/daily_vals/: %d\n", length(processed_rds_dates)))
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cat(sprintf(" Dates needing processing: %d\n", length(dates_to_process_migration)))
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if (length(dates_to_process_migration) > 0) {
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assign("dates_to_process", dates_to_process_migration, envir = .GlobalEnv)
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cat(sprintf(" Will process: %s to %s\n", dates_to_process_migration[1], dates_to_process_migration[length(dates_to_process_migration)]))
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}
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}
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source("r_app/20_ci_extraction_per_field.R")
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main()
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# Verify output
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field_tiles_ci_verify <- file.path("laravel_app", "storage", "app", project_dir, "field_tiles_CI")
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tiff_count <- 0
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if (dir.exists(field_tiles_ci_verify)) {
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field_dirs_verify <- list.dirs(field_tiles_ci_verify, full.names = TRUE, recursive = FALSE)
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if (length(field_dirs_verify) > 0) {
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all_files_verify <- list.files(field_dirs_verify, pattern = "^\\d{4}-\\d{2}-\\d{2}\\.tif$")
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tiff_count <- length(all_files_verify)
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}
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}
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cat(sprintf("✓ Script 20 completed - %d CI TIFFs in field_tiles_CI/\n", tiff_count))
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}, error = function(e) {
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cat("✗ Error in Script 20:", e$message, "\n")
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pipeline_success <<- FALSE
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})
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} else if (skip_20) {
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cat("\n========== SKIPPING SCRIPT 20 (CI already extracted) ==========\n")
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}
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# ==============================================================================
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# SCRIPT 30: INTERPOLATE GROWTH MODEL
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# ==============================================================================
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if (pipeline_success) {
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cat("\n========== RUNNING SCRIPT 30: INTERPOLATE GROWTH MODEL ==========\n")
|
|
tryCatch({
|
|
# Set environment variables for the script
|
|
assign("end_date", end_date, envir = .GlobalEnv)
|
|
assign("offset", offset, envir = .GlobalEnv)
|
|
assign("project_dir", project_dir, envir = .GlobalEnv)
|
|
|
|
source("r_app/30_interpolate_growth_model.R")
|
|
main() # Call main() to execute the script with the environment variables
|
|
|
|
# Verify interpolated output
|
|
growth_dir <- file.path("laravel_app", "storage", "app", project_dir, "growth_model_interpolated")
|
|
if (dir.exists(growth_dir)) {
|
|
files <- list.files(growth_dir, pattern = "\\.rds$|\\.csv$")
|
|
cat(sprintf("✓ Script 30 completed - generated %d growth model files\n", length(files)))
|
|
} else {
|
|
cat("✓ Script 30 completed\n")
|
|
}
|
|
}, error = function(e) {
|
|
cat("✗ Error in Script 30:", e$message, "\n")
|
|
pipeline_success <<- FALSE
|
|
})
|
|
}
|
|
|
|
# ==============================================================================
|
|
# SCRIPT 21: CONVERT CI RDS TO CSV (uses Script 30 output)
|
|
# ==============================================================================
|
|
if (pipeline_success && !skip_21) {
|
|
cat("\n========== RUNNING SCRIPT 21: CONVERT CI RDS TO CSV ==========\n")
|
|
tryCatch({
|
|
# Set environment variables for the script
|
|
assign("end_date", end_date, envir = .GlobalEnv)
|
|
assign("offset", offset, envir = .GlobalEnv)
|
|
assign("project_dir", project_dir, envir = .GlobalEnv)
|
|
|
|
source("r_app/21_convert_ci_rds_to_csv.R")
|
|
main() # Call main() to execute the script with the environment variables
|
|
|
|
# Verify CSV output was created
|
|
ci_csv_path <- file.path("laravel_app", "storage", "app", project_dir, "ci_extracted")
|
|
if (dir.exists(ci_csv_path)) {
|
|
csv_files <- list.files(ci_csv_path, pattern = "\\.csv$")
|
|
cat(sprintf("✓ Script 21 completed - converted to %d CSV files\n", length(csv_files)))
|
|
} else {
|
|
cat("✓ Script 21 completed\n")
|
|
}
|
|
}, error = function(e) {
|
|
cat("✗ Error in Script 21:", e$message, "\n")
|
|
pipeline_success <<- FALSE
|
|
})
|
|
} else if (skip_21) {
|
|
cat("\n========== SKIPPING SCRIPT 21 (CSV already created) ==========\n")
|
|
}
|
|
|
|
# ==============================================================================
|
|
# PYTHON 31: HARVEST IMMINENT WEEKLY
|
|
# ==============================================================================
|
|
if (pipeline_success) {
|
|
cat("\n========== RUNNING PYTHON 31: HARVEST IMMINENT WEEKLY ==========\n")
|
|
tryCatch({
|
|
# Run Python script in pytorch_gpu conda environment
|
|
# Script expects positional project name (not --project flag)
|
|
# Run from smartcane root so conda can find the environment
|
|
cmd <- sprintf('conda run -n pytorch_gpu python python_app/31_harvest_imminent_weekly.py %s', project_dir)
|
|
cat("DEBUG: Running command:", cmd, "\n")
|
|
result <- system(cmd)
|
|
|
|
if (result == 0) {
|
|
# Verify harvest output - check for THIS WEEK's specific file
|
|
current_week <- as.numeric(format(end_date, "%V"))
|
|
current_year <- as.numeric(format(end_date, "%Y"))
|
|
expected_file <- file.path("laravel_app", "storage", "app", project_dir, "reports", "kpis", "field_stats",
|
|
sprintf("%s_harvest_imminent_week_%02d_%d.csv", project_dir, current_week, current_year))
|
|
|
|
if (file.exists(expected_file)) {
|
|
cat(sprintf("✓ Script 31 completed - generated harvest imminent file for week %02d\n", current_week))
|
|
} else {
|
|
cat("✓ Script 31 completed (check if harvest.xlsx is available)\n")
|
|
}
|
|
} else {
|
|
cat("⚠ Script 31 completed with errors (check harvest.xlsx availability)\n")
|
|
}
|
|
}, error = function(e) {
|
|
setwd(original_dir)
|
|
cat("⚠ Script 31 error:", e$message, "\n")
|
|
})
|
|
}
|
|
|
|
# ==============================================================================
|
|
# SCRIPT 40: MOSAIC CREATION
|
|
# ==============================================================================
|
|
if (pipeline_success && !skip_40) {
|
|
cat("\n========== RUNNING SCRIPT 40: MOSAIC CREATION ==========\n")
|
|
tryCatch({
|
|
# Set environment variables for the script
|
|
assign("end_date", end_date, envir = .GlobalEnv)
|
|
assign("offset", offset, envir = .GlobalEnv)
|
|
assign("project_dir", project_dir, envir = .GlobalEnv)
|
|
|
|
source("r_app/40_mosaic_creation_per_field.R")
|
|
main() # Call main() to execute the script with the environment variables
|
|
|
|
# Verify mosaic output
|
|
mosaic_dir <- file.path("laravel_app", "storage", "app", project_dir, "weekly_tile_max", "5x5")
|
|
if (dir.exists(mosaic_dir)) {
|
|
files <- list.files(mosaic_dir, pattern = "\\.tif$")
|
|
cat(sprintf("✓ Script 40 completed - generated %d mosaic files\n", length(files)))
|
|
} else {
|
|
cat("✓ Script 40 completed\n")
|
|
}
|
|
}, error = function(e) {
|
|
cat("✗ Error in Script 40:", e$message, "\n")
|
|
pipeline_success <<- FALSE
|
|
})
|
|
} else if (skip_40) {
|
|
cat("\n========== SKIPPING SCRIPT 40 (mosaics already created) ==========\n")
|
|
}
|
|
|
|
# ==============================================================================
|
|
# SCRIPT 80: CALCULATE KPIs
|
|
# ==============================================================================
|
|
if (pipeline_success) { # Always run Script 80 - it calculates KPIs for the current week
|
|
cat("\n========== RUNNING SCRIPT 80: CALCULATE KPIs ==========\n")
|
|
tryCatch({
|
|
# Set environment variables for the script (Script 80's main() uses these as fallbacks)
|
|
# NOTE: end_date is already a Date, just assign directly without as.Date()
|
|
assign("end_date", end_date, envir = .GlobalEnv)
|
|
assign("end_date_str", end_date_str, envir = .GlobalEnv)
|
|
assign("offset", offset, envir = .GlobalEnv)
|
|
assign("project_dir", project_dir, envir = .GlobalEnv)
|
|
|
|
source("r_app/80_calculate_kpis.R")
|
|
main() # Call main() to execute the script with the environment variables
|
|
|
|
# Verify KPI output
|
|
kpi_dir <- file.path("laravel_app", "storage", "app", project_dir, "reports", "kpis", "field_stats")
|
|
if (dir.exists(kpi_dir)) {
|
|
files <- list.files(kpi_dir, pattern = "\\.csv$|\\.json$")
|
|
cat(sprintf("✓ Script 80 completed - generated %d KPI files\n", length(files)))
|
|
} else {
|
|
cat("✓ Script 80 completed\n")
|
|
}
|
|
}, error = function(e) {
|
|
cat("✗ Error in Script 80:", e$message, "\n")
|
|
cat("Full error:\n")
|
|
print(e)
|
|
pipeline_success <<- FALSE
|
|
})
|
|
}
|
|
|
|
# ==============================================================================
|
|
# SCRIPT 90/91: GENERATE WORD REPORTS (CLIENT-TYPE SPECIFIC)
|
|
# ==============================================================================
|
|
if (pipeline_success) {
|
|
# Determine client type from project mapping
|
|
source("r_app/parameters_project.R")
|
|
source("r_app/00_common_utils.R")
|
|
client_type <- get_client_type(project_dir)
|
|
|
|
if (client_type == "agronomic_support") {
|
|
# SCRIPT 90: Agronomic Support Report (for Aura)
|
|
cat("\n========== RUNNING SCRIPT 90: AGRONOMIC SUPPORT REPORT (WORD) ==========\n")
|
|
tryCatch({
|
|
# Render the R Markdown file with parameters
|
|
# The Rmd file will load parameters_project and utilities internally
|
|
rmarkdown::render(
|
|
"r_app/90_CI_report_with_kpis_simple.Rmd",
|
|
params = list(
|
|
data_dir = project_dir,
|
|
report_date = end_date,
|
|
mail_day = "Monday",
|
|
borders = TRUE,
|
|
ci_plot_type = "both",
|
|
colorblind_friendly = FALSE,
|
|
facet_by_season = FALSE,
|
|
x_axis_unit = "days"
|
|
),
|
|
output_file = sprintf("SmartCane_Report_agronomic_%s_%s.docx", project_dir, end_date_str),
|
|
output_dir = file.path("laravel_app", "storage", "app", project_dir, "reports"),
|
|
quiet = FALSE,
|
|
knit_root_dir = getwd()
|
|
)
|
|
|
|
# Verify report was created
|
|
report_file <- file.path("laravel_app", "storage", "app", project_dir, "reports",
|
|
sprintf("SmartCane_Report_agronomic_%s_%s.docx", project_dir, end_date_str))
|
|
if (file.exists(report_file)) {
|
|
cat(sprintf("✓ Script 90 completed - generated Word report: %s\n", basename(report_file)))
|
|
} else {
|
|
cat("⚠ Script 90 report file not found - check rendering\n")
|
|
}
|
|
}, error = function(e) {
|
|
cat("✗ Error in Script 90:", e$message, "\n")
|
|
print(e)
|
|
pipeline_success <<- FALSE
|
|
})
|
|
} else if (client_type == "cane_supply") {
|
|
# SCRIPT 91: Cane Supply Report (for Angata, Chemba, Xinavane, ESA)
|
|
cat("\n========== RUNNING SCRIPT 91: CANE SUPPLY REPORT (WORD) ==========\n")
|
|
tryCatch({
|
|
# Render the R Markdown file with parameters
|
|
# The Rmd file will load parameters_project and utilities internally
|
|
rmarkdown::render(
|
|
"r_app/91_CI_report_with_kpis_Angata.Rmd",
|
|
params = list(
|
|
data_dir = project_dir,
|
|
report_date = end_date,
|
|
mail_day = "Monday",
|
|
borders = TRUE,
|
|
ci_plot_type = "both",
|
|
colorblind_friendly = FALSE,
|
|
facet_by_season = FALSE,
|
|
x_axis_unit = "days"
|
|
),
|
|
output_file = sprintf("SmartCane_Report_cane_supply_%s_%s.docx", project_dir, end_date_str),
|
|
output_dir = file.path("laravel_app", "storage", "app", project_dir, "reports"),
|
|
quiet = FALSE,
|
|
knit_root_dir = getwd()
|
|
)
|
|
|
|
# Verify report was created
|
|
report_file <- file.path("laravel_app", "storage", "app", project_dir, "reports",
|
|
sprintf("SmartCane_Report_cane_supply_%s_%s.docx", project_dir, end_date_str))
|
|
if (file.exists(report_file)) {
|
|
cat(sprintf("✓ Script 91 completed - generated Word report: %s\n", basename(report_file)))
|
|
} else {
|
|
cat("⚠ Script 91 report file not found - check rendering\n")
|
|
}
|
|
}, error = function(e) {
|
|
cat("✗ Error in Script 91:", e$message, "\n")
|
|
print(e)
|
|
pipeline_success <<- FALSE
|
|
})
|
|
}
|
|
}
|
|
|
|
# ==============================================================================
|
|
# SUMMARY
|
|
# ==============================================================================
|
|
cat("\n========== PIPELINE COMPLETE ==========\n")
|
|
cat(sprintf("Project: %s\n", project_dir))
|
|
cat(sprintf("End Date: %s\n", end_date_str))
|
|
cat(sprintf("Offset: %d days\n", offset))
|
|
if (pipeline_success) {
|
|
cat("Status: ✓ All scripts completed successfully\n")
|
|
} else {
|
|
cat("Status: ✗ Pipeline failed - check errors above\n")
|
|
}
|
|
cat("Pipeline sequence: Python Download → R 10 → R 20 → R 30 → R 21 → Python 31 → R 40 → R 80 → R 90/91\n")
|