From 7082dce54f6e98d91af7e0db83db126f9674221c Mon Sep 17 00:00:00 2001 From: Nathan Layman Date: Fri, 11 Oct 2024 07:10:54 -0700 Subject: [PATCH] More pipeline bug fixes. --- .env | Bin 733 -> 733 bytes R/create_ndvi_date_lookup.R | 8 +- R/get_outbreak_history.R | 2 +- R/get_outbreak_history_animation.R | 44 +- _targets.R | 25 +- _targets/meta/meta | 3627 ++++++++++++----- data/modis_ndvi_transformed/.gitkeep | 0 .../modis_ndvi_bundle_request.RDS | Bin 390448 -> 390448 bytes renv.lock | 12 +- 9 files changed, 2712 insertions(+), 1006 deletions(-) delete mode 100644 data/modis_ndvi_transformed/.gitkeep diff --git a/.env b/.env index 1e6686c47ab6f2ffefaeb033f6c37141d840c758..8c7aac58c846b364db76987f373ba1a8cc469e54 100644 GIT binary patch literal 733 zcmV<30wVnYM@dveQdv+`02>iN=mS?>v6mhJAo7R(DsFMoTHT@$)&!1ntGL`EWwt3j zCrZ<&O@`NCn3_9(M%KHr7E8M6P-t-a0R`5$Rn)G=gAkUGa7g@s@2Jb)Vca_Qdr_E; zgDQzsf3`WDyI?vZnF|=J6N8IBaz9caeDc7dam!VYxyMheoJIfZ?{qE8Ib1 z4XG-OKL^SI8+&^C@B6s`lWYOJD1^SU3(%3#g7K>+Y8LPyiET+w+PUfcuw*Y9Mch=B4;~cCcJyyCTIN3SQ(zZnfV6dMby98G7;}~((~Vrba)5(=+Hf^>2Gr~r!5&LRx*?q*Gx>^U z2#NuiONi^1^UF4hgg3q?QrbVHE_x@n8m@Vweb6DCsOq{DjZBcRdCF-tLQJk46} z&f(Cc9dS0SKW$dA1D9|X@JaODcq+O$$J-)x7oNw1U&&&Fk zBkt-B2To;YUz@rE%JGbyPy(eelOTQQt6aMzGmx zyJej}yajj9|EvSO zC6EYBycmlGCGHMsD{Y4vyUKUZcQ)-Kc_$2swB}yja2!M;T9Q4_+1s$6+`t%o>!;Ae zG9%M>vIXGnmbqStz?zr`jE#j;(n>1mc5E+dTWq>CYYk06a#<4tcC4!DvRbz0mSzg( zB<)J5WZ;NJ*OX#rjW$)HmxLtFTPYP0CjpK2g&G)qTKNMe{{`XWpe1(swrx%+7XW<| zIXQ7;^xw@z1+Hf!d-_xuu!S@XAUr{X1b-lr^)DCbS#O@92yrqs{4(}2r}nT3sH;?Q zJGPXe(XpPphsf{_yQ1rnmq0h&s`CSL17jXff~GJ9vKmGwW)7*H$(1c*eZ~o0_WfXg z7n_ROgmShfxbm6|AO@YT_eB0+4S1BNHpe084)(fq^x0jckd zfiq6}(SZMP&Gx~a zlHmv7NFzL6J{kmM5&CXt2hgeEN1=C|jcU1PgtLSb`QTo5F9pPPqXd PfPSg93hZUVb5VV#OcG>b diff --git a/R/create_ndvi_date_lookup.R b/R/create_ndvi_date_lookup.R index de57f07..d362354 100644 --- a/R/create_ndvi_date_lookup.R +++ b/R/create_ndvi_date_lookup.R @@ -11,13 +11,11 @@ #' @author Emma Mendelsohn #' @export create_ndvi_date_lookup <- function(sentinel_ndvi_transformed, - sentinel_ndvi_transformed_directory, - modis_ndvi_transformed, - modis_ndvi_transformed_directory) { + modis_ndvi_transformed) { # Connect to Sentinel and Modis datasets - sentinel_dataset <- arrow::open_dataset(list.files(sentinel_ndvi_transformed_directory, pattern = "*.parquet", full.names = TRUE)) - modis_dataset <- arrow::open_dataset(list.files(modis_ndvi_transformed_directory, pattern = "*.parquet", full.names = TRUE)) + sentinel_dataset <- arrow::open_dataset(sentinel_ndvi_transformed) + modis_dataset <- arrow::open_dataset(modis_ndvi_transformed) # Sentinel dates handling ------------------------------------------------- diff --git a/R/get_outbreak_history.R b/R/get_outbreak_history.R index 933fef3..34fb923 100644 --- a/R/get_outbreak_history.R +++ b/R/get_outbreak_history.R @@ -63,7 +63,7 @@ get_daily_outbreak_history <- function(dates_df, # Check if outbreak_history file exist and can be read and that we don't want to overwrite them. if(!is.null(error_safe_read_parquet(outbreak_history_filename)) & !overwrite & year != year(Sys.time())) { - message("preprocessed landcover parquet file already exists and can be loaded, skipping download and processing") + message("preprocessed outbreak history parquet file already exists and can be loaded, skipping download and processing") return(outbreak_history_filename) } diff --git a/R/get_outbreak_history_animation.R b/R/get_outbreak_history_animation.R index 0a006e1..e91e6b6 100644 --- a/R/get_outbreak_history_animation.R +++ b/R/get_outbreak_history_animation.R @@ -25,6 +25,7 @@ get_outbreak_history_animation <- function(wahis_outbreak_history, wahis_outbreak_history_animations_directory, num_cores = 1, + overwrite = FALSE, ...) { output_basename = tools::file_path_sans_ext(basename(wahis_outbreak_history)) @@ -35,29 +36,36 @@ get_outbreak_history_animation <- function(wahis_outbreak_history, # Fastest way to use parquet files is to do as many opperations before collect or pull min_weight <- outbreak_history_dataset |> summarise(min_weight = min(weight, na.rm = TRUE)) |> - pull(min_weight) + pull(min_weight, as_vector = TRUE) max_weight <- outbreak_history_dataset |> summarise(max_weight = max(weight, na.rm = TRUE)) |> - pull(max_weight) + pull(max_weight, as_vector = TRUE) # Identify limits (used to calibrate the color scale) lims <- c(min_weight, max_weight) # Keep as much as possible out of memory and on disk. Arrow permits fast access. - time_frames <- outbreak_history_dataset |> select(time_frame) |> distinct() |> pull(time_frame) + time_frames <- outbreak_history_dataset |> select(time_frame) |> distinct() |> pull(time_frame, as_vector = TRUE) + + # Create temporary directory if it does not yet exist + tmp_dir <- paste(wahis_outbreak_history_animations_directory, output_basename, sep = "/") + dir.create(tmp_dir, recursive = TRUE, showWarnings = FALSE) # Make animations for both recent and old outbreaks - map(time_frames, function(tf) { + output_files <- map(time_frames, function(tf) { - output_filename = file.path(wahis_outbreak_history_animations_directory, glue::glue("{output_basename}_{tf}.gif")) - message(paste("Animating", basename(output_filename))) + output_filename = file.path(wahis_outbreak_history_animations_directory, glue::glue("{basename(output_basename)}_{tf}.gif")) - dates <- outbreak_history_dataset |> filter(time_frame == tf) |> select(date) |> distinct() |> pull(date) - - # Create temporary directory if it does not yet exist - tmp_dir <- paste(wahis_outbreak_history_animations_directory, output_basename, sep = "/") - dir.create(tmp_dir, recursive = TRUE, showWarnings = FALSE) + # Check if outbreak_history file exist and can be read and that we don't want to overwrite them. + if(file.exists(output_filename) & !overwrite) { + message(glue::glue("{basename(output_filename)} already exists. Skipping.")) + return(output_filename) + } + + message(paste("Animating", basename(output_filename))) + + dates <- outbreak_history_dataset |> filter(time_frame == tf) |> select(date) |> distinct() |> pull(date, as_vector = TRUE) # This function makes a png for each date which will then get stiched together # into the animation. Saving each png is faster than trying to do everything @@ -67,9 +75,10 @@ get_outbreak_history_animation <- function(wahis_outbreak_history, function(d) plot_outbreak_history(outbreak_history_dataset |> filter(date == d) |> filter(time_frame == tf) |> - collect(), - tmp_dir = tmp_dir, - lims = lims)) |> + collect(), + tmp_dir = tmp_dir, + write_frame = TRUE, + lims = lims)) |> unlist() |> sort() # Add in a delay at end before looping back to beginning. This is in frames not seconds @@ -81,12 +90,17 @@ get_outbreak_history_animation <- function(wahis_outbreak_history, gif_file = output_filename) # Clean up temporary files - unlink(tmp_dir, recursive = T) + file.remove(png_files) # Return the location of the rendered animation output_filename } ) + + # Clean up temporary files + unlink(tmp_dir, recursive = T) + + return(output_files) } #' Plot Outbreak History diff --git a/_targets.R b/_targets.R index 591df36..b61501a 100644 --- a/_targets.R +++ b/_targets.R @@ -294,7 +294,6 @@ dynamic_targets <- tar_plan( wahis_outbreak_history_AWS), # Enforce Dependency pattern = map(wahis_outbreak_dates), error = "null", # Keep going if error. It will be caught next time the pipeline is run. - format = "file", repository = "local"), @@ -320,12 +319,11 @@ dynamic_targets <- tar_plan( wahis_outbreak_history_animations_directory), # Just included to enforce dependency with wahis_outbreak_history pattern = map(wahis_outbreak_history), error = "null", - format = "file", repository = "local"), - # - # tar_target(wahis_outbreak_history_animations_AWS_upload, AWS_put_files(wahis_outbreak_history_animations, - # wahis_outbreak_history_animations_directory), - # error = "null"), # Continue the pipeline even on error + + tar_target(wahis_outbreak_history_animations_AWS_upload, AWS_put_files(wahis_outbreak_history_animations, + wahis_outbreak_history_animations_directory), + error = "null"), # Continue the pipeline even on error # SENTINEL NDVI ----------------------------------------------------------- # 2018-present @@ -378,11 +376,8 @@ dynamic_targets <- tar_plan( tar_target(modis_ndvi_bundle_request, submit_modis_ndvi_bundle_request(modis_ndvi_token, modis_ndvi_task_id_continent, modis_ndvi_bundle_request_file) |> - rowwise() |> - tar_group(), - cue = tar_cue("always"), - iteration = "group" - ), + filter(grepl("NDVI", file_name)), + cue = tar_cue("always")), # Check if modis_ndvi files already exists on AWS and can be loaded # The only important one is the directory. The others are there to enforce dependencies. @@ -623,12 +618,8 @@ data_targets <- tar_plan( # ndvi anomalies -------------------------------------------------- - tar_target(ndvi_date_lookup, - create_ndvi_date_lookup(sentinel_ndvi_transformed, - sentinel_ndvi_transformed_directory, - modis_ndvi_transformed, - modis_ndvi_transformed_directory)), - + tar_target(ndvi_date_lookup, create_ndvi_date_lookup(sentinel_ndvi_transformed, + modis_ndvi_transformed)), tar_target(ndvi_historical_means_directory, create_data_directory(directory_path = "data/ndvi_historical_means")), diff --git a/_targets/meta/meta b/_targets/meta/meta index 8f30c68..9ff058b 100644 --- a/_targets/meta/meta +++ b/_targets/meta/meta @@ -1,5 +1,5 @@ name|type|data|command|depend|seed|path|time|size|bytes|format|repository|iteration|parent|children|seconds|warnings|error -.Random.seed|object|21edc3c54349dcb4||||||||||||||| +.Random.seed|object|1aaab1764a202d00||||||||||||||| aggregate_augmented_data_by_adm|function|2315722e5d2c9d69||||||||||||||| aggregated_data_rsa|pattern|6dbb43f34bc42ac8|ea0a3280c45817ae||-1696630435||||137860|qs|aws|vector||aggregated_data_rsa_94f732f8*aggregated_data_rsa_5e501efa*aggregated_data_rsa_34327510*aggregated_data_rsa_40e9884c*aggregated_data_rsa_5ababfa3|288.617|| aggregated_data_rsa_34327510|branch|c1e4fd089c317f41|ea0a3280c45817ae|1b56fcad8b0f2922|1726064958|bucket=open-rvfcast-data*region=us-east-1*key=_targets/aggregated_data_rsa_34327510*endpoint=TlVMTA*version=|t19755.8889066061s||27572|qs|aws|vector|aggregated_data_rsa||56.413|| @@ -479,10 +479,10 @@ create_ecmwf_forecasts_dataset|function|557bbbb473a2eb1c||||||||||||||| create_example_target|function|df4f421d40047080||||||||||||||| create_modis_ndvi_dataset|function|ed26259cdf3f08e1||||||||||||||| create_nasa_weather_dataset|function|7eb26dcea55b80b9||||||||||||||| -create_ndvi_date_lookup|function|c36d9fd6104d7695||||||||||||||| 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-get_daily_outbreak_history|function|635647bf4c1caba2||||||||||||||| +get_daily_outbreak_history|function|598fcf68186e5b5c||||||||||||||| get_daily_weights|function|46164f96da4404c8||||||||||||||| get_distance_weights|function|573ecd900e5a64d0||||||||||||||| get_ecmwf_forecasts_AWS|stem|a619b1f9e3d38dec|348639ecc76f53f5|da0bfdb91967a1a3|715056382|bucket=open-rvfcast*region=us-east-1*key=_targets/objects/get_ecmwf_forecasts_AWS*endpoint=TlVMTA*version=|t20004.2866766633s||30|qs|aws|vector|||0.103|| @@ -3214,7 +3214,7 @@ get_nasa_weather_coordinates|function|37d517f8f8c205a8||||||||||||||| get_outbreak_distance_matrix|function|f385d13a21259a5a||||||||||||||| get_outbreak_distance_weights|function|dde97ff3b7afe35e||||||||||||||| get_outbreak_history|function|0515c34f4109a803||||||||||||||| -get_outbreak_history_animation|function|6b9e836b956483b0||||||||||||||| +get_outbreak_history_animation|function|40045f1c1f1a32d2||||||||||||||| 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