changes

laravel_app/app/Http/Controllers/ProjectController.php

@@ -15,7 +15,7 @@ public function index()
     public function show(string $projectName,?string $currentTab = null)
     {
         if($project = Project::firstWhere([['name',$projectName]])) {
-            $availableTabs = ['downloads', 'mosaics', 'reports', 'mailings', 'settings'];
+            $availableTabs = ['downloads', 'mosaics', 'reports', 'mailings', 'settings', 'exports'];
             return in_array($currentTab, $availableTabs) ? view('projects.show', compact(['project', 'currentTab'])) : redirect(route('project.show', [$projectName,'downloads']));
         }
         return abort(404);

laravel_app/app/Jobs/ProjectInterpolateGrowthModelJob.php

@@ -16,9 +16,8 @@
 class ProjectInterpolateGrowthModelJob implements ShouldQueue
 {
     use Batchable, Dispatchable, InteractsWithQueue, Queueable, SerializesModels;
+
     protected Project $project;
-    protected Carbon $date;
-    protected int $offset;
 
     public function __construct(Project $project)
     {

laravel_app/app/Jobs/newDownloadsUploaded.php

@@ -0,0 +1,32 @@
+<?php
+
+namespace App\Jobs;
+
+use Illuminate\Bus\Queueable;
+use Illuminate\Contracts\Queue\ShouldQueue;
+use Illuminate\Foundation\Bus\Dispatchable;
+use Illuminate\Queue\InteractsWithQueue;
+use Illuminate\Queue\SerializesModels;
+
+class newDownloadsUploaded implements ShouldQueue
+{
+    use Dispatchable, InteractsWithQueue, Queueable, SerializesModels;
+
+    private Project $project;
+
+    /**
+     * Create a new job instance.
+     */
+    public function __construct(Project $project)
+    {
+        $this->project = $project;
+    }
+
+    /**
+     * Execute the job.
+     */
+    public function handle(): void
+    {
+       $this->project->newDownloadsUploaded();
+    }
+}

laravel_app/app/Livewire/Projects/Tabs/Exports.php

@@ -0,0 +1,56 @@
+<?php
+
+namespace App\Livewire\Projects\Tabs;
+
+use App\Models\Project;
+use Livewire\Component;
+
+class Exports extends Component
+{
+    public Project $project;
+    public $formData = [];
+
+    public $showDownloadTifsModal = false;
+    public $showDownloadMosaicsModal = false;
+
+
+    public function mount()
+    {
+        $this->formData = [
+            'start_date' => now()->subDays(6)->format('Y-m-d'),
+            'end_date'   => now()->subDay()->format('Y-m-d'),
+        ];
+    }
+
+
+
+    public function render()
+    {
+        return view('livewire.projects.tabs.exports');
+    }
+
+    public function downloadRds()
+    {
+        return $this->project->getRdsAsDownload();
+    }
+
+    public function downloadTifs()
+    {
+        $startDate = \Carbon\Carbon::parse($this->formData['start_date']);
+        $endDate = \Carbon\Carbon::parse($this->formData['end_date']);
+        $this->showDownloadTifsModal = false;
+        return $this->project->getTifsAsZip(
+            $startDate, $endDate
+        );
+    }
+
+    public function downloadMosaics()
+    {
+        $startDate = \Carbon\Carbon::parse($this->formData['start_date']);
+        $endDate = \Carbon\Carbon::parse($this->formData['end_date']);
+        $this->showDownloadMosaicsModal = false;
+        return $this->project->getMosaicsAsZip(
+            $startDate, $endDate
+        );
+    }
+}

laravel_app/app/Models/Project.php

@@ -2,6 +2,7 @@
 
 namespace App\Models;
 
+use App\Jobs\ProjectDownloadRDSJob;
 use App\Jobs\ProjectDownloadTiffJob;
 use App\Jobs\ProjectInterpolateGrowthModelJob;
 use App\Jobs\ProjectMosiacGeneratorJob;
@@ -348,7 +349,7 @@ public function getFileDownloadsFor(Carbon $endDate, int $offset = 7): array
     public function getMosaicsFor(Carbon $endDate, int $offset = 7): array
     {
         return collect(range(0, 3))
-            ->map(function() use ($endDate, $offset){
+            ->map(function () use ($endDate, $offset) {
                 $currentEndDate = $endDate->clone();
                 if (!$currentEndDate->isDayOfWeek($this->mail_day)) {
                     $endDate->previous($this->mail_day);
@@ -402,4 +403,101 @@ private function getMinimumDateFromHarvestExcelFile(): Carbon
             return min($carry, Carbon::instance(SharedDate::excelToDateTimeObject($value[$season_start_index])));
         }, now());
     }
+
+    public function newDownloadsUploaded()
+    {
+//        $this->createDownloadRecordsInDatabaseAndUpdateStatusForAllDownloadedImages();
+        $date = Carbon::parse('2023-01-01');
+        $now = Carbon::now();
+
+        $offset = (int) $date->diffInDays($now);
+//        dispatch_sync(new ProjectDownloadRDSJob($this, Carbon::yesterday(), 1));
+        dispatch_sync(new ProjectInterpolateGrowthModelJob($this));
+    }
+    public function getRdsAsDownload() {
+
+        $path = $this->download_path.'/Data/extracted_ci/cumulative_vals/combined_CI_data.rds';
+
+        return Storage::download(
+            $path, 'combined_CI_data.rds'
+        );
+    }
+
+    public function getTifsAsZip(Carbon $startDate, Carbon $endDate) {
+        $path = $this->download_path.'/merged_final_tif';
+        $files = collect(Storage::files($path))
+            ->filter(fn($file) => Str::endsWith($file, '.tif'))
+            ->filter(function ($file) use ($startDate, $endDate) {
+                $dateString = str_replace('.tif', '', basename($file));
+                $date = Carbon::parse($dateString);
+                return $date->between($startDate, $endDate);
+            });
+
+        return $this->createZipArchiveAndReturn($files);
+    }
+
+    public function getMosaicsAsZip(Carbon $startDate, Carbon $endDate) {
+        $path = $this->download_path.'/weekly_mosaic';
+
+        // create a collection of all week numbers and years for given date range
+        $allowedFiles = collect(CarbonPeriod::create($startDate, $endDate)->toArray())
+            ->map(fn($date) => sprintf('week_%s_%s.tif',$date->weekOfYear, $date->year))
+            ->unique();
+
+
+        $files = collect(Storage::files($path))
+            ->filter(fn($file) => Str::endsWith($file, '.tif'))
+            ->filter(function ($file) use ($allowedFiles) {
+                return $allowedFiles->contains(basename($file));
+            });
+        putenv('TMPDIR='.storage_path('app'));
+
+        return $this->createZipArchiveAndReturn($files);
+    }
+
+    private function createZipArchiveAndReturn(Collection $files)
+    {
+        $zipPath = storage_path('app/'.$this->download_path.'/download.zip');
+        $zip = new \ZipArchive();
+        $zip->open($zipPath, \ZipArchive::CREATE | \ZipArchive::OVERWRITE);
+        $files->each(function ($file) use ($zip) {
+            $zip->addFile(storage_path('app/'.$file), basename($file));
+        });
+        $zip->close();
+
+        return response()->download(
+            $zipPath, 'download.zip'
+        );
+    }
+
+    public function createDownloadRecordsInDatabaseAndUpdateStatusForAllDownloadedImages(): void
+    {
+        $merged_tiffs = $this->getMergedTiffList();
+        $this->downloads->each(function ($download) use ($merged_tiffs) {
+            if ($merged_tiffs->contains($download->path) && $download->status !== 'success') {
+                $download->setStatusSuccess();
+            }
+        });
+
+        $merged_tiffs->each(function ($path) {
+            if ($this->downloads()->where('path', $path)->count() === 0) {
+                $this->downloads()->create([
+                    'path'   => $path,
+                    'status' => 'success',
+                    'name'   => explode('/', $path)[count(explode('/', $path)) - 1]
+                ]);
+            }
+        });
+    }
+
+    public function createAllMosaicsInDatabaseAndUpdateStatusForAllDownloadedImages()
+    {
+       $list_of_desired_mosaics = $this->getMergedTiffList()
+           ->map(fn($file) => str_replace('.tif', '', basename($file) ))
+           ->map(function($date) {
+             $carbon = Carbon::parse($date);
+              return sprintf('week_%s_%s', $carbon->format('W'), $carbon->year);
+           })
+           ->unique();
+    }
 }

laravel_app/resources/views/components/download-mosaics-as-zip-modal.blade.php

@@ -0,0 +1,47 @@
+@props([
+    'formData',
+])
+
+<x-modal wire:model.live="showDownloadMosaicsModal" {{ $attributes }} >
+    <x-form-modal submit="downloadMosaics" wire:loading.class="opacity-50">
+        <x-slot name="title">
+            {{ __('Download Mosaics') }}
+        </x-slot>
+
+        <x-slot name="description">
+        </x-slot>
+
+
+        <x-slot name="form">
+            <div class="col-span-6 sm:col-span-4">
+                <x-label for="start_date" value="{{ __('Start Date') }}"/>
+                <x-input id="start_date" type="date" max="{{\Carbon\Carbon::yesterday()->toDateString()}}" class="mt-1 block w-full" wire:model.live="formData.start_date" autofocus/>
+                <x-input-error for="formData.start_date" class="mt-2"/>
+            </div><div class="col-span-6 sm:col-span-4">
+                <x-label for="end_date" value="{{ __('End Date') }}"/>
+                <x-input id="end_date" type="date" max="{{\Carbon\Carbon::yesterday()->toDateString()}}" class="mt-1 block w-full" wire:model.live="formData.end_date" />
+                <x-input-error for="formData.end_date" class="mt-2"/>
+            </div>
+            <div>
+                <span class="whitespace-nowrap"></span>
+            </div>
+        </x-slot>
+
+        <x-slot name="actions">
+            <x-action-message class="mr-3" on="saved">
+                {{ __('Saved.') }}
+            </x-action-message>
+
+            <x-secondary-button class="mr-3"
+                                type="button"
+                                x-on:click="$wire.showDownloadMosaicsModal = false"
+            >
+                {{ __('Cancel') }}
+            </x-secondary-button>
+            <x-button wire:loading.disabled>
+                {{ __('Download') }}
+            </x-button>
+
+        </x-slot>
+    </x-form-modal>
+</x-modal>

laravel_app/resources/views/components/download-tifs-as-zip-modal.blade.php

@@ -0,0 +1,47 @@
+@props([
+    'formData',
+])
+
+<x-modal wire:model.live="showDownloadTifsModal" {{ $attributes }} >
+    <x-form-modal submit="downloadTifs" wire:loading.class="opacity-50">
+        <x-slot name="title">
+            {{ __('Download Zip with satelite data') }}
+        </x-slot>
+
+        <x-slot name="description">
+        </x-slot>
+
+
+        <x-slot name="form">
+            <div class="col-span-6 sm:col-span-4">
+                <x-label for="start_date" value="{{ __('Start Date') }}"/>
+                <x-input id="start_date" type="date" max="{{\Carbon\Carbon::yesterday()->toDateString()}}" class="mt-1 block w-full" wire:model.live="formData.start_date" autofocus/>
+                <x-input-error for="formData.start_date" class="mt-2"/>
+            </div><div class="col-span-6 sm:col-span-4">
+                <x-label for="end_date" value="{{ __('End Date') }}"/>
+                <x-input id="end_date" type="date" max="{{\Carbon\Carbon::yesterday()->toDateString()}}" class="mt-1 block w-full" wire:model.live="formData.end_date" />
+                <x-input-error for="formData.end_date" class="mt-2"/>
+            </div>
+            <div>
+                <span class="whitespace-nowrap"></span>
+            </div>
+        </x-slot>
+
+        <x-slot name="actions">
+            <x-action-message class="mr-3" on="saved">
+                {{ __('Saved.') }}
+            </x-action-message>
+
+            <x-secondary-button class="mr-3"
+                                type="button"
+                                x-on:click="$wire.showDownloadTifsModal = false"
+            >
+                {{ __('Cancel') }}
+            </x-secondary-button>
+            <x-button wire:loading.disabled>
+                {{ __('Save') }}
+            </x-button>
+
+        </x-slot>
+    </x-form-modal>
+</x-modal>

laravel_app/resources/views/livewire/projects/menu.blade.php

@@ -4,4 +4,5 @@
     <a class=" capitalize font-semibold text-md hover:rounded-lg hover:bg-gray-50 hover:text-indigo-600 hover:border-0 py-2 pl-2 pr-3 leading-6 whitespace-nowrap gap-2 flex items-baseline group text-gray-700 {{!($activeTab == 'reports')   ?: 'rounded-lg bg-gray-50 text-indigo-600 border-0'}}" href="{{route('project.show',[$projectName,'reports'])}}"><i class="group-hover:text-indigo-600 w-6 text-gray-400 fg-map-stat fg-lg"></i>Reports</a>
     <a class=" capitalize font-semibold text-md hover:rounded-lg hover:bg-gray-50 hover:text-indigo-600 hover:border-0 py-2 pl-2 pr-3 leading-6 whitespace-nowrap gap-2 flex items-baseline group text-gray-700 {{!($activeTab == 'mailings')  ?: 'rounded-lg bg-gray-50 text-indigo-600 border-0'}}" href="{{route('project.show',[$projectName,'mailings'])}}"><i class="group-hover:text-indigo-600 w-6 text-gray-400 fa-regular fa-envelope"></i>Mailings</a>
     <a class=" capitalize font-semibold text-md hover:rounded-lg hover:bg-gray-50 hover:text-indigo-600 hover:border-0 py-2 pl-2 pr-3 leading-6 whitespace-nowrap gap-2 flex items-baseline group text-gray-700 {{!($activeTab == 'settings')  ?: 'rounded-lg bg-gray-50 text-indigo-600 border-0'}}" href="{{route('project.show',[$projectName,'settings'])}}"><i class="group-hover:text-indigo-600 w-6 text-gray-400 fa-solid fa-gear"></i>Settings</a>
+    <a class=" capitalize font-semibold text-md hover:rounded-lg hover:bg-gray-50 hover:text-indigo-600 hover:border-0 py-2 pl-2 pr-3 leading-6 whitespace-nowrap gap-2 flex items-baseline group text-gray-700 {{!($activeTab == 'exports')  ?: 'rounded-lg bg-gray-50 text-indigo-600 border-0'}}" href="{{route('project.show',[$projectName,'exports'])}}"><i class="group-hover:text-indigo-600 w-6 text-gray-400 fa-solid fa-download"></i>Exports</a>
 </div>

laravel_app/resources/views/livewire/projects/tabs/exports.blade.php

@@ -0,0 +1,56 @@
+<div class="flex flex-col divide-y space-y-4 m-2">
+    <div id="edit" class="flex flex-col md:flex-row gap-2">
+        <div class="flex flex-col md:w-1/3">
+            <div class="text-xl font-bold ">
+                {{ __('RDS File') }}
+            </div>
+            <div class="text-gray-500 text-md">
+                {{__('Download the RDS file for this project')}}
+            </div>
+        </div>
+        <div class="md:w-2/3">
+            <button wire:click="downloadRds" class="inline-flex items-center rounded-md bg-indigo-600 px-2.5 py-1.5 text-sm font-semibold text-white shadow-sm hover:bg-indigo-500 focus-visible:outline focus-visible:outline-2 focus-visible:outline-offset-2 focus-visible:outline-indigo-600" >Download RDS</button>
+        </div>
+    </div>
+    <div
+         class="flex flex-col md:flex-row">
+        <div class="flex flex-col my-4 md:w-1/3">
+            <span class="text-xl font-bold dark:text-gray-300">{{__('Download Tifs')}}</span>
+            <div class="text-gray-500 text-md">
+                {{ __('Create a zip file with satelite images for a given time series') }}
+            </div>
+        </div>
+        <div id="mail" class="flex flex-col md:w-2/3" > {{-- flex col--}}
+            <div class="flex justify-between my-4">
+                <div class="inline-flex items-center gap-2">
+                    <div class=" text-md font-bold">
+            <button x-on:click="$wire.showDownloadTifsModal = true" class="inline-flex items-center rounded-md bg-indigo-600 px-2.5 py-1.5 text-sm font-semibold text-white shadow-sm hover:bg-indigo-500 focus-visible:outline focus-visible:outline-2 focus-visible:outline-offset-2 focus-visible:outline-indigo-600" >Download tifs</button>
+                    </div>
+                </div>
+            </div>
+            <div class="flex w-full "></div>
+        </div>
+    </div>
+    <div
+        class="flex flex-col md:flex-row">
+        <div class="flex flex-col my-4 md:w-1/3">
+            <span class="text-xl font-bold dark:text-gray-300">{{__('Download Mosaics')}}</span>
+            <div class="text-gray-500 text-md">
+                {{ __('Create a zip file with mosaic images for a given time series') }}
+            </div>
+        </div>
+        <div id="mail" class="flex flex-col md:w-2/3" > {{-- flex col--}}
+            <div class="flex justify-between my-4">
+                <div class="inline-flex items-center gap-2">
+                    <div class=" text-md font-bold">
+                        <button x-on:click="$wire.showDownloadMosaicsModal = true" class="inline-flex items-center rounded-md bg-indigo-600 px-2.5 py-1.5 text-sm font-semibold text-white shadow-sm hover:bg-indigo-500 focus-visible:outline focus-visible:outline-2 focus-visible:outline-offset-2 focus-visible:outline-indigo-600" >Download Mosaics</button>
+                    </div>
+                </div>
+            </div>
+            <div class="flex w-full "></div>
+        </div>
+    </div>
+    <div class="flex justify-end items-center py-4"></div>
+    <x-download-mosaics-as-zip-modal :formData="$formData"></x-download-mosaics-as-zip-modal>
+    <x-download-tifs-as-zip-modal :formData="$formData"></x-download-tifs-as-zip-modal>
+</div>

laravel_app/resources/views/projects/show.blade.php

@@ -24,6 +24,9 @@
                 @case('settings')
                     <livewire:projects.tabs.settings :project="$project"></livewire:projects.tabs.settings>
                     @break
+                @case('exports')
+                    <livewire:projects.tabs.exports :project="$project"></livewire:projects.tabs.exports>
+                    @break
                 @default
                         <div class="flex w-full h-screen justify-center items-center"> Menu Component not found.</div>
             @endswitch

laravel_app/tests/Unit/Models/ProjectTest.php

@@ -329,4 +329,5 @@ public static function scheduleDayProvider()
         ];
 
     }
+
 }

r_app/CI_report_dashboard_planet.Rmd

@@ -230,20 +230,20 @@ create_CI_map <- function(pivot_raster, pivot_shape, pivot_spans, show_legend =
   tm_shape(pivot_raster, unit = "m")+
   tm_raster(breaks = c(0,0.5,1,2,3,4,5,6,7,Inf), palette = "RdYlGn",legend.is.portrait = legend_is_portrait ,midpoint = NA) +
   tm_layout(main.title = paste0("\nMax CI week ", week,"\n",  age, " weeks old"),
-            main.title.size = 0.7, legend.show = show_legend) +
+            main.title.size = 0.7, legend.show = show_legend) # +
-  tm_shape(pivot_shape) +
+  # tm_shape(pivot_shape) +
-  tm_borders(lwd = 3) +  tm_text("sub_field", size = 1/2) +
+  # tm_borders(lwd = 3) +  tm_text("sub_field", size = 1/2) +
-  tm_shape(pivot_spans) + tm_borders(lwd = 0.5, alpha=0.5)
+  # tm_shape(pivot_spans) + tm_borders(lwd = 0.5, alpha=0.5)
 }
 
 create_CI_diff_map <- function(pivot_raster, pivot_shape, pivot_spans, show_legend = F, legend_is_portrait = F, week_1, week_2, age){
   tm_shape(pivot_raster, unit = "m")+
   tm_raster(breaks = c(-3,-2,-1,0,1,2, 3), palette = "RdYlGn",legend.is.portrait = legend_is_portrait ,midpoint = 0, title = "CI difference") +
   tm_layout(main.title =  paste0("CI change week ", week_1, "- week ",week_2, "\n", age," weeks old"),
-            main.title.size = 0.7, legend.show = show_legend) +
+            main.title.size = 0.7, legend.show = show_legend) # +
-  tm_shape(pivot_shape) +
+ # tm_shape(pivot_shape) +
-  tm_borders(lwd = 3) +  tm_text("sub_field", size = 1/2) +
+ # tm_borders(lwd = 3) +  tm_text("sub_field", size = 1/2) +
-  tm_shape(pivot_spans) + tm_borders(lwd = 0.5, alpha=0.5)
+ # tm_shape(pivot_spans) + tm_borders(lwd = 0.5, alpha=0.5)
 }
 
 ci_plot <- function(pivotName){

r_app/interpolate_growth_model.R

@@ -27,8 +27,6 @@ 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")
@@ -53,7 +51,7 @@ pivot_stats2 <- readRDS(here(cumulative_CI_vals_dir,"combined_CI_data.rds")) %>%
 # gather data into long format for easier calculation and visualisation
 pivot_stats_long <- pivot_stats2 %>%
   tidyr::gather("Date", value, -field, -sub_field ) %>%
-  mutate(Date = right(Date, 8),
+  mutate(#Date = right(Date, 8),
          Date = lubridate::ymd(Date)
   ) %>%
   drop_na(c("value","Date")) %>%
@@ -72,7 +70,7 @@ pivot_stats_long <- pivot_stats2 %>%
 # pivot_select_model_Data_2023 <- harvesting_data %>% filter(year == 2023) %>% filter(!is.na(season_start))  %>% pull(sub_field)
 
 pivot_select_model_Data_2024 <- harvesting_data %>% filter(year == 2024)%>% filter(!is.na(season_start)) %>% pull(sub_field)
-print(pivot_select_model_Data_2024)
+message(pivot_select_model_Data_2024)
 # pivots_dates_Data_2022 <- pivots_dates0 %>% filter(!is.na(season_end_2022))
 # pivot_select_model_Data_2022 <- unique(pivots_dates_Data_2022$pivot_quadrant )
 #
@@ -83,14 +81,14 @@ print(pivot_select_model_Data_2024)
 # pivot_select_model_Data_2024 <- unique(pivots_dates_Data_2024$pivot_quadrant)
 
 extract_CI_data <- function(field_names, harvesting_data, field_CI_data, season) {
-  #  field_names =  "4042902"
+  #  field_names =  "Nandi A1a"
   #  field_names =  "1.13A"
   #  harvesting_data = harvesting_data
   # field_CI_data = pivot_stats_long
   #  season= 2024
 
   filtered_harvesting_data <- harvesting_data %>%
-    na.omit() %>%
+  #  na.omit() %>%
     filter(year == season, sub_field %in% field_names)
 
   filtered_field_CI_data <- field_CI_data %>%
@@ -125,6 +123,7 @@ extract_CI_data <- function(field_names, harvesting_data, field_CI_data, season)
 # message('2023')
 Data_2024 <- map(pivot_select_model_Data_2024, ~ extract_CI_data(.x, harvesting_data = harvesting_data, field_CI_data = pivot_stats_long, season = 2024)) %>% list_rbind()
 message('2024')
+head(Data_2024)
 
 
 #CI_all <- rbind(Data_2023, Data_2024)

r_app/parameters_project.R

@@ -92,7 +92,7 @@ if(project_dir == "chemba"){
    names(field_boundaries_sf) <- c("field", "sub_field", "geometry")
    field_boundaries <- field_boundaries_sf %>% vect()
    harvesting_data <- read_excel(here(data_dir, "harvest.xlsx"),
-                col_types = c("numeric", "numeric", "numeric",
+                col_types = c("text", "text", "numeric",
                               "date", "date", "numeric", "text",
                               "numeric", "numeric")) %>%
                  mutate(season_end = case_when(