added log as project file;

laravel_app/app/Jobs/ProjectDownloadRDSJob.php

@@ -3,6 +3,7 @@
 namespace App\Jobs;
 
 use App\Models\Project;
+use App\ProjectLogger;
 use Carbon\Carbon;
 use Illuminate\Bus\Batchable;
 use Illuminate\Bus\Queueable;
@@ -44,10 +45,10 @@ public function handle(): void
         $process->run();
 
         if (!$process->isSuccessful()) {
-            logger('error', [$process->getErrorOutput()]);
+            ProjectLogger::log($this->project, $process->getErrorOutput());
             return;
         }
-        logger($process->getOutput());
+        ProjectLogger::log($this->project, $process->getOutput());
 
     }
 
@@ -58,7 +59,7 @@ public static function fromDate(Project $project,Carbon $date,int $offset = 1):N
     {
         $filename = $date->format('Y-m-d') . '.tif';
         if (!$project->downloads()->statusSuccess()->where(['name' => $filename])->exists()) {
-            Log::warning("The download $filename can't be processed. Please check it's status.");
+            ProjectLogger::log($project, "The download $filename can't be processed. Please check it's status.");
             return new NullJob();
         }
         return new self($project,$date,$offset);

laravel_app/app/Jobs/ProjectDownloadTiffJob.php

@@ -4,6 +4,7 @@
 
 use App\Models\Project;
 use App\Models\ProjectDownload;
+use App\ProjectLogger;
 use Illuminate\Bus\Batchable;
 use Illuminate\Bus\Queueable;
 use Illuminate\Contracts\Queue\ShouldQueue;
@@ -49,13 +50,15 @@ public function handle(): void
         $process->setTimeout(600);
         $process->run();
 
+        $project = $this->download->project;
+
         if (!$process->isSuccessful()) {
-            logger('error', [$process->getErrorOutput()]);
+            ProjectLogger::log($project, $process->getErrorOutput());
             $this->download->setStatusFailed();
             return;
         }
         // Success
-        logger($process->getOutput());
+        ProjectLogger::log($project, $process->getOutput());
         $this->download->setStatusSuccess();
         dispatch(ProjectDownloadRDSJob::fromDate($this->download->project, $this->date, $this->days));
     }

laravel_app/app/Jobs/ProjectInterpolateGrowthModelJob.php

@@ -3,6 +3,7 @@
 namespace App\Jobs;
 
 use App\Models\Project;
+use App\ProjectLogger;
 use Carbon\Carbon;
 use Illuminate\Bus\Batchable;
 use Illuminate\Bus\Queueable;
@@ -23,7 +24,7 @@ class ProjectInterpolateGrowthModelJob implements ShouldQueue
 
     public function __construct(Project $project)
     {
-        logger(__CLASS__ . __METHOD__);
+        ProjectLogger::log($project, __CLASS__ . __METHOD__);
         $this->project = $project;
     }
 
@@ -32,7 +33,7 @@ public function __construct(Project $project)
      */
     public function handle(): void
     {
-        logger('start interpolate growth model', [$this->project->name]);
+        ProjectLogger::log($this->project,'start interpolate growth model', [$this->project->name]);
         $command = [
             sprintf('%s/interpolate_growth_model.sh', base_path('../')),
             sprintf('--project_dir=%s', $this->project->download_path),
@@ -43,10 +44,10 @@ public function handle(): void
         $process->run();
 
         if (!$process->isSuccessful()) {
-            logger('error', [$process->getErrorOutput()]);
+            ProjectLogger::log($this->project,  $process->getErrorOutput());
             return;
         }
-        logger($process->getOutput());
+        ProjectLogger::log($this->project, $process->getOutput());
 
     }
 }

laravel_app/app/Jobs/ProjectMosiacGeneratorJob.php

@@ -4,6 +4,7 @@
 
 use App\Models\Project;
 use App\Models\ProjectMosaic;
+use App\ProjectLogger;
 use Carbon\Carbon;
 use Illuminate\Bus\Batchable;
 use Illuminate\Bus\Queueable;
@@ -45,6 +46,7 @@ public function __construct(ProjectMosaic $mosaic)
     public function handle(): void
     {
         $projectFolder = base_path('../');
+        $project = $this->mosaic->project;
 
         $command = [
             sprintf('%sbuild_mosaic.sh', $projectFolder),
@@ -53,20 +55,23 @@ public function handle(): void
             sprintf('--data_dir=%s', $this->mosaic->project->download_path),
             sprintf('--file_name_tif=%s', basename($this->mosaic->path)),
         ];
+
+        ProjectLogger::log($project, 'command:'. print_r($command, true));
+
         $currentPath = '/usr/bin:/usr/gnu/bin:/usr/local/bin:/bin:/usr/bin/Users/mfolkerts/anaconda3/bin:/Library/Apple/usr/bin';
 
         try {
             $process = ProcessNew::timeout(220)
                 ->env(['PATH' => $currentPath.':/usr/local/Cellar/pandoc/3.1.8/bin/pandoc'])
-                ->start($command, function (string $type, string $output) {
+                ->start($command, function (string $type, string $output) use ($project) {
-                    logger($output);
+                    ProjectLogger::log($project, $output);
                 });
             $results = $process->wait();
             if ($results->successful()) {
                 $this->mosaic->setStatusSuccess();
             }
         } catch (\RuntimeException|ProcessTimedOutException|ProcessFailedException $e) {
-            echo $e->getMessage();
+            ProjectLogger::log($project, $e->getMessage());
             $this->mosaic->setStatusFailed();
         }
     }
@@ -77,13 +82,13 @@ public function handle(): void
     public static function handleFor(Project $project, Carbon $endDate, int $offset): NullJob|ProjectMosiacGeneratorJob
     {
         $endDate = $endDate->clone();
-        logger("ProjectMosiacGeneratorJob::handleFor($endDate, $offset)");
+        ProjectLogger::log($project, "ProjectMosiacGeneratorJob::handleFor($endDate, $offset)");
         if ($project->hasInvalidMosaicFor($endDate, $offset)) {
-            logger("ProjecMosaicGeneratorJob::handleFor(end_date: $endDate, offset: $offset): InvalidMosaic.");
+            ProjectLogger::log($project,"ProjecMosaicGeneratorJob::handleFor(end_date: $endDate, offset: $offset): InvalidMosaic.");
             return new NullJob();
         }
 
-        logger(__CLASS__."::".__METHOD__."::Project->mail_day::".$project->mail_day);
+        ProjectLogger::log($project, __CLASS__."::".__METHOD__."::Project->mail_day::".$project->mail_day);
 
         if (Carbon::parse($project->mail_day)->dayOfWeek < $endDate->dayOfWeek) {
             $endDate->next($project->mail_day);

laravel_app/app/Jobs/ProjectReportGeneratorJob.php

@@ -4,6 +4,7 @@
 
 use App\Livewire\Forms\MailingForm;
 use App\Models\ProjectReport;
+use App\ProjectLogger;
 use Illuminate\Bus\Batchable;
 use Illuminate\Bus\Queueable;
 use Illuminate\Contracts\Queue\ShouldBeUnique;
@@ -50,7 +51,7 @@ public function handle()
             sprintf('--data_dir=%s', $this->projectReport->project->download_path),
             sprintf('--borders=%s', $this->projectReport->project->borders ? 'True' : 'False'),
         ];
-        logger('command:'. print_r($command, true));
+        ProjectLogger::log($this->projectReport->project, 'command:'. print_r($command, true));
 
         // Convert commands array to a single string
 
@@ -65,7 +66,7 @@ public function handle()
             $process->wait(function ($type, $buffer) use (&$myOutput) {
 //                $this->stream(to: 'processOutput', content: $buffer);
                 $myOutput[] = $buffer;
-                logger($buffer);
+                ProjectLogger::log($this->projectReport->project, $buffer);
             });
             $this->processOutput = collect($myOutput)->join('\n');
             $this->projectReport->setStatusSuccess();

laravel_app/app/Jobs/newDownloadsUploaded.php

@@ -2,6 +2,7 @@
 
 namespace App\Jobs;
 
+use App\Models\Project;
 use Illuminate\Bus\Queueable;
 use Illuminate\Contracts\Queue\ShouldQueue;
 use Illuminate\Foundation\Bus\Dispatchable;

laravel_app/app/Models/Project.php

@@ -477,7 +477,6 @@ public function newDownloadsUploaded()
 
     public function getRdsAsDownload()
     {
-
         $path = $this->download_path.'/Data/extracted_ci/cumulative_vals/combined_CI_data.rds';
 
         return Storage::download(

laravel_app/app/ProjectLogger.php

@@ -0,0 +1,16 @@
+<?php
+
+namespace App;
+
+use App\Models\Project;
+use Illuminate\Support\Facades\Storage;
+
+class ProjectLogger
+{
+    public static function log(Project $project, $message)
+    {
+        $filePath = $project->download_path . '/logs/' . now()->format('Ymd') . '.log';
+        Storage::makeDirectory(dirname($filePath));
+        file_put_contents(Storage::path($filePath), now()->format('Y-m-d H:i:s') . ': ' . $message . PHP_EOL, FILE_APPEND);
+    }
+}

r_app/CI_report_dashboard_planet.Rmd

@@ -52,30 +52,14 @@ library(caret)
 library(randomForest)
 library(CAST)
 
-# source(here("r_app/report_utils.R"))
 source("report_utils.R")
 
-
 ```
 
 ```{r directories, message=FALSE, warning=FALSE, include=FALSE}
 project_dir <- params$data_dir
-# laravel_storage_dir <- here("laravel_app/storage/app/",params$data_dir)
-laravel_storage_dir <- here("laravel_app/storage/app",project_dir)
-
-data_dir <- here(laravel_storage_dir, "Data")
-# message('DATA_DIR',data_dir)
-extracted_CI_dir <- here(data_dir, "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")
-
-weekly_CI_mosaic <- here(laravel_storage_dir, "weekly_mosaic")
-
 source(here("r_app", "parameters_project.R"))
 
-
-
 log_message("Starting the R Markdown script")
 log_message(paste("mail_day params:",  params$mail_day))
 log_message(paste("report_date params:",  params$report_date))

r_app/ci_extraction.R

@@ -1,5 +1,4 @@
 # nolint start: commented_code_linter, line_length_linter,object_usage_linter.
-library(here)
 library(sf)
 library(terra)
 library(tidyverse)
@@ -18,7 +17,7 @@ if (length(args) == 0) {
 # Converteer het eerste argument naar een numerieke waarde
 end_date <- as.Date(args[1])
 if (is.na(end_date)) {
-end_date <- lubridate::dmy("28-08-2024")
+    end_date <- lubridate::dmy("28-08-2024")
 }
 
 offset <- as.numeric(args[2])
@@ -36,42 +35,10 @@ project_dir <- as.character(args[3])
 if (!is.character(project_dir)) {
   project_dir <- "chemba"
 }
-
-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 = FALSE
-planet_tif_folder <- here(laravel_storage_dir, "merged_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")
-daily_CI_vals_dir <- here(extracted_CI_dir, "daily_vals")
-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")
-
-# source(here("r_app/parameters_project.R"))
-# source(here("r_app/ci_extraction_utils.R"))
-# source(here("r_app/mosaic_creation_utils.R"))
 
 source("parameters_project.R")
 source("ci_extraction_utils.R")
-# source("mosaic_creation_utils.R")
-
-dir.create(here(laravel_storage_dir))
-dir.create(here(data_dir))
-dir.create(here(extracted_CI_dir))
-dir.create(here(daily_CI_vals_dir))
-dir.create(here(cumulative_CI_vals_dir))
-dir.create(here(weekly_CI_mosaic))
-dir.create(here(daily_vrt))
-dir.create(merged_final)
-dir.create(harvest_dir)
 
 dates <- date_list(end_date, offset)
 print(dates)

r_app/interpolate_growth_model.R

@@ -1,17 +1,12 @@
-
-library(here)
 library(sf)
 library(terra)
 library(tidyverse)
 library(lubridate)
 library(exactextractr)
-# library(readxl)
-
 
 # Vang alle command line argumenten op
 args <- commandArgs(trailingOnly = TRUE)
 
-
 # Converteer het tweede argument naar een string waarde
 project_dir <- as.character(args[1])
 
@@ -20,27 +15,6 @@ if (!is.character(project_dir)) {
   project_dir <- "chemba"
 }
 
-
-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 = FALSE
-
-data_dir <- here(laravel_storage_dir, "Data")
-extracted_CI_dir <- here(data_dir, "extracted_ci")
-daily_CI_vals_dir <- here(extracted_CI_dir, "daily_vals")
-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")
-
-# source(here("r_app/parameters_project.R"))
-# source(here("r_app/ci_extraction_utils.R"))
-# source(here("r_app/mosaic_creation_utils.R"))
-
 source("parameters_project.R")
 source("ci_extraction_utils.R")
 

r_app/mosaic_creation.R

@@ -1,19 +1,7 @@
-# activeer de renv omgeving;
-
-# renv::activate('~/smartCane/r_app')
-# renv::restore()
-
-
-
-library(here)
 library(sf)
 library(terra)
 library(tidyverse)
 library(lubridate)
-# library(exactextractr)
-# library(readxl)
-#funcion CI_prep package
-
 
 # Vang alle command line argumenten op
 args <- commandArgs(trailingOnly = TRUE)
@@ -42,51 +30,11 @@ if (!is.character(project_dir)) {
   project_dir <- "chemba"
 }
 
-
-laravel_storage_dir <- here("laravel_app/storage/app", project_dir)
-#preparing directories
-reports_dir <- here(laravel_storage_dir, "reports")
-planet_tif_folder <- here(laravel_storage_dir, "merged_tif")
-merged_final <- here(laravel_storage_dir, "merged_final_tif")
-
-new_project_question = FALSE
-planet_tif_folder <- here(laravel_storage_dir, "merged_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")
-daily_CI_vals_dir <- here(extracted_CI_dir, "daily_vals")
-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")
-
-# source(here("r_app/parameters_project.R"))
-# source(here("r_app/mosaic_creation_utils.R"))
-
 source("parameters_project.R")
 source("mosaic_creation_utils.R")
 
-# dir.create(here(laravel_storage_dir))
-# dir.create(here(reports_dir))
-# dir.create(here(data_dir))
-# dir.create(here(extracted_CI_dir))
-# dir.create(here(daily_CI_vals_dir))
-# dir.create(here(cumulative_CI_vals_dir))
-# dir.create(here(weekly_CI_mosaic))
-# dir.create(here(daily_vrt))
-# dir.create(merged_final)
-# dir.create(harvest_dir)
-
-# end_date <- lubridate::dmy("28-8-2024")
 week <- week(end_date)
 
-
-#weeks_ago = 0
-
-# Creating weekly mosaic
-#dates <- date_list(weeks_ago)
 dates <- date_list(end_date, offset)
 
 file_name_tif <- as.character(args[4])

r_app/parameters_project.R

@@ -1,7 +1,33 @@
-
+library(here)
 library('readxl')
 #chemba
 
+laravel_storage_dir <- here("laravel_app/storage/app", project_dir)
+reports_dir <- here(laravel_storage_dir, "reports")
+log_dir <- here(laravel_storage_dir, "logs")
+planet_tif_folder <- here(laravel_storage_dir, "merged_tif")
+merged_final <- here(laravel_storage_dir, "merged_final_tif")
+planet_tif_folder <- here(laravel_storage_dir, "merged_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")
+daily_CI_vals_dir <- here(extracted_CI_dir, "daily_vals")
+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(laravel_storage_dir), showWarnings = FALSE)
+dir.create(here(data_dir), showWarnings = FALSE)
+dir.create(here(log_dir), showWarnings = FALSE)
+dir.create(here(extracted_CI_dir), showWarnings = FALSE)
+dir.create(here(daily_CI_vals_dir), showWarnings = FALSE)
+dir.create(here(cumulative_CI_vals_dir), showWarnings = FALSE)
+dir.create(here(weekly_CI_mosaic),showWarnings = FALSE)
+dir.create(here(daily_vrt), showWarnings = FALSE)
+dir.create(merged_final,showWarnings = FALSE)
+dir.create(harvest_dir,showWarnings = FALSE)
+
 field_boundaries_sf <- st_read(here(data_dir, "pivot.geojson"))
 
 names(field_boundaries_sf) <- c("field", "sub_field", "geometry")
@@ -36,8 +62,7 @@ harvesting_data <- read_excel(here(data_dir, "harvest.xlsx")) %>%
     age = round(as.numeric(season_end - season_start) / 7, 0)
   )
 
-# Define the log file path
+log_file <- here(log_dir, paste0("log_", format(Sys.Date(), "%Y%m%d"), ".log"))
-log_file <- here("laravel_app/storage/app/rmd_log.txt")
 
 # Create a logging function
 log_message <- function(message) {