added rule for missing mergedTifs;

build_mosaic.sh

@@ -0,0 +1,30 @@
+#!/bin/bash
+
+filename="report_dummie.docx"
+weeks_ago="0"
+report_date="2022-12-12"
+
+# Parse de command line argumenten
+while [ "$#" -gt 0 ]; do
+    case "$1" in
+        --weeks_ago=*)
+            weeks_ago="${1#*=}"
+            ;;
+        *)
+            echo "Onbekende optie: $1"
+            exit 1
+            ;;
+    esac
+    shift
+done
+
+# Controleer of de vereiste argumenten zijn ingesteld
+if [ -z "$filename" ] || [ -z "$weeks_ago" ] || [ -z $report_date ]; then
+    echo "Missende argumenten. Gebruik: build_reports.sh --filename=hello.txt --weeks_ago=3 --report_date=2020-01-01"
+    exit 1
+fi
+
+
+echo "Weeks ago: $weeks_ago"
+cd /Users/mfolkerts/smartCane/r_app
+Rscript 2_CI_data_prep.R $weeks_ago

build_report.sh

@@ -1,15 +1,51 @@
 #!/bin/bash
-## Runnen van Rmd bestand
+
-# -e betekent "evalueren" en -i specificeert de input file
+filename="report_dummie.docx"
-Rscript --version
+weeks_ago="0"
-echo $PATH
+report_date="2022-12-12"
+
+# Parse de command line argumenten
+while [ "$#" -gt 0 ]; do
+    case "$1" in
+        --filename=*)
+            filename="${1#*=}"
+            ;;
+        --weeks_ago=*)
+            weeks_ago="${1#*=}"
+            ;;
+        --report_date=*)
+            report_date="${1#*=}"
+            ;;
+        *)
+            echo "Onbekende optie: $1"
+            exit 1
+            ;;
+    esac
+    shift
+done
+
+# Controleer of de vereiste argumenten zijn ingesteld
+if [ -z "$filename" ] || [ -z "$weeks_ago" ] || [ -z $report_date ]; then
+    echo "Missende argumenten. Gebruik: build_reports.sh --filename=hello.txt --weeks_ago=3 --report_date=2020-01-01"
+    exit 1
+fi
+
+# Je script logica hier
+echo "Filename: $filename"
+echo "Weeks ago: $weeks_ago"
+echo "Report date: $report_date"
+
 #script_dir="$(dirname "$0")"
 #echo $script_dir;
 #/bin/ps aux | grep fontd
+#output_file="/Users/mfolkerts/smartCane/laravel_app/storage/app/chemba/$filename"
 
+#echo "Output file: $output_file"
 echo '\n'
 
 echo 'zx28tb' | /usr/bin/sudo -S launchctl load -w /System/Library/LaunchAgents/com.apple.fontd.useragent.plist
 cd /Users/mfolkerts/smartCane/r_app
-Rscript -e "rmarkdown::render('/Users/mfolkerts/smartCane/r_app/CI_Report_dashboard_planet.Rmd', 'all')"
+#Rscript -e "rmarkdown::render('/Users/mfolkerts/smartCane/r_app/CI_Report_dashboard_planet.Rmd', 'all')"
-
+#Rscript 1_harvest_data_EcoFarm_v2.R
+Rscript 2_CI_data_prep.R $weeks_ago
+Rscript -e "rmarkdown::render('CI_report_dashboard_planet.Rmd', output_file='$filename', params=list(ref='$ref', report_date='$report_date'))"

laravel_app/app/Jobs/ProjectMosiacGeneratorJob.php

@@ -0,0 +1,69 @@
+<?php
+
+namespace App\Jobs;
+
+use App\Models\Project;
+use App\Models\ProjectReport;
+use Illuminate\Bus\Queueable;
+use Illuminate\Contracts\Queue\ShouldBeUnique;
+use Illuminate\Contracts\Queue\ShouldQueue;
+use Illuminate\Foundation\Bus\Dispatchable;
+use Illuminate\Queue\InteractsWithQueue;
+use Illuminate\Queue\SerializesModels;
+use Symfony\Component\Process\Process;
+
+class ProjectMosiacGeneratorJob implements ShouldQueue
+{
+    use Dispatchable, InteractsWithQueue, Queueable, SerializesModels;
+
+
+    public $year;
+    public $week;
+    public Project $project;
+    /**
+     * Create a new job instance.
+     */
+    public function __construct(Project $project, $year, $week)
+    {
+        $this->year = $year;
+        $this->week = $week;
+        //
+    }
+
+    /**
+     * Execute the job.
+     */
+    public function handle(): void
+    {
+        $weeksAgo = ProjectReport::weeksAgoForYearAndWeek($this->year, $this->week);
+
+        $projectFolder = base_path('../');
+
+        $command = [
+            sprintf('%sbuild_mosaic.sh', $projectFolder),
+            sprintf('--weeks_ago=%s', $weeksAgo),
+        ];
+
+
+        $process = new Process($command);
+        $process->setTimeout(120);
+        $currentPath = '/usr/gnu/bin:/usr/local/bin:/bin:/usr/bin/Users/mfolkerts/anaconda3/bin:/Library/Apple/usr/bin';
+
+        $process->setEnv(['PATH' => $currentPath.':/usr/local/Cellar/pandoc/3.1.8/bin/pandoc']);
+//        $process->setTimeout(36000); // stel een geschikte timeout in
+        $process->start();
+        try {
+            $myOutput = [];
+            $process->wait(function ($type, $buffer) use (&$myOutput) {
+//                $this->stream(to: 'processOutput', content: $buffer);
+                $myOutput[] = $buffer;
+                logger($buffer);
+            });
+            $this->processOutput = collect($myOutput)->join('\n');
+
+        } catch (ProcessFailedException $exception) {
+            echo $exception->getMessage();
+
+        }
+    }
+}

laravel_app/app/Livewire/Projects/MosaicManager.php

@@ -0,0 +1,58 @@
+<?php
+
+namespace App\Livewire\Projects;
+
+use App\Jobs\ProjectMosiacGeneratorJob;
+use App\Models\Project;
+use Livewire\Component;
+
+class MosaicManager extends Component
+{
+    public $project;
+
+    public $formData = [
+        'week' => '',
+        'year' => '',
+    ];
+    public $showCreateModal = false;
+
+    public function mount(Project $project) {
+        $this->path = $project->download_path;
+    }
+
+    public function render()
+    {
+        return view('livewire.projects.mosaic-manager', [
+            'downloads' => $this->project
+        ]);
+    }
+
+    public function saveMosiac(){
+        $this->validate([
+            'formData.year' => 'required',
+            'formData.week' => 'required',
+        ]);
+
+        ProjectMosiacGeneratorJob::dispatch($this->project, $this->formData['year'], $this->formData['week']);
+
+        $this->showCreateModal = false;
+    }
+
+    public function openCreateMosiacsModal(){
+        $this->showCreateModal = true;
+    }
+
+    public function getDateRangeProperty()
+    {
+        if (empty($this->formData['week']) || strlen($this->formData['year']) !== 4) {
+            return '<span class="text-red-500">Invalid week or year</span>';
+        }
+        $begin = now()
+            ->setISODate($this->formData['year'], $this->formData['week'])
+            ->startOfWeek();
+        $end = now()
+            ->setISODate($this->formData['year'], $this->formData['week'])
+            ->endOfWeek();
+        return $begin->format('Y-m-d').' - '.$end->format('Y-m-d');
+    }
+}

laravel_app/app/Models/Project.php

@@ -5,6 +5,7 @@
 use Illuminate\Database\Eloquent\Factories\HasFactory;
 use Illuminate\Database\Eloquent\Model;
 use Illuminate\Support\Carbon;
+use Illuminate\Support\Collection;
 use Illuminate\Support\Facades\Storage;
 use Illuminate\Support\Str;
 
@@ -143,7 +144,7 @@ public function allMosaicsPresent(Carbon $endDate)
         $mosaicsNotPresentInFilesystem = $this->getMosiacFilenameListByEndDate($endDate)
             ->filter(function ($filename) {
                 return !$this->getMosaicList()->contains(function ($mosaicFilename) use ($filename) {
-                    return Str::endsWith( $mosaicFilename, substr($filename, -16));
+                    return Str::endsWith($mosaicFilename, substr($filename, -16));
                 });
             });
         if ($mosaicsNotPresentInFilesystem->count() === 0) {
@@ -173,5 +174,52 @@ public function getMosiacFilenameListByEndDate(Carbon $endDate): \Illuminate\Sup
         return $result;
     }
 
+    public function getMosiacList()
+    {
+        return collect(Storage::files($this->getMosaicPath()))
+            ->filter(fn($file) => Str::endsWith($file, '.tif'))
+            ->sortByDesc(function ($file) {
+                $parts = explode('_', str_replace('.tif', '', $file));
+                $week = $parts[1];
+                $year = $parts[2];
+                return $year.sprintf('%02d', $week);
+            })
+            ->values();
+    }
 
+    public static function getAllDatesOfWeeksInYear($year, $weekNumber): Collection
+    {
+        $startOfWeek = Carbon::now()->setISODate($year, $weekNumber)->startOfWeek();
+        $dates = collect([]);
+
+        for ($day = 0; $day < 7; $day++) {
+            $dates->push((clone $startOfWeek)->addDays($day)->toDateString());
+        }
+
+        return $dates;
+    }
+
+    public function allMergedTiffsPresent(Collection $haystack, Collection $needles)
+    {
+        $needlesNotInHaystack = $needles->filter(function ($needle) use ($haystack) {
+            return !$haystack->contains(function ($item) use ($needle) {
+                return str_contains($item, $needle);
+            });
+        });
+
+        if ($needlesNotInHaystack->count() > 0) {
+            $message = sprintf(
+                'Missing merged tiffs: %s',
+                $needlesNotInHaystack->implode(', ')
+            );
+
+            throw new \Exception($message);
+        }
+        return true;
+    }
+
+    public function getMergedTiffList()
+    {
+        return collect([]);;
+    }
 }

laravel_app/app/Models/ProjectReport.php

@@ -29,7 +29,12 @@ public function project()
 
     public function weeksAgo()
     {
-        return now()->diffInWeeks(now()->setISODate($this->year, $this->week));
+        return $this->weeksAgoForYearAndWeek($this->year, $this->week);
+    }
+
+    public static function weeksAgoForYearAndWeek($year, $week)
+    {
+        return now()->diffInWeeks(now()->setISODate($year, $week));
     }
 
     public function getFileName()

laravel_app/app/Rules/AllMergedTiffsPresentRule.php

@@ -0,0 +1,36 @@
+<?php
+
+namespace App\Rules;
+
+use Illuminate\Contracts\Validation\Rule;
+use App\Models\Project;
+use App\Models\ProjectReport;
+
+class AllMergedTiffsPresentRule implements Rule
+{
+    protected $project;
+    protected $errorMessage = '';
+
+    public function __construct(Project $project)
+    {
+        $this->project = $project;
+    }
+
+    public function passes($attribute, $value)
+    {
+        try {
+            return $this->project->allMergedTiffsPresent(
+                $this->project->getMergedTiffList(),
+                Project::getAllDatesOfWeeksInYear($value['year'], $value['week'])
+            );
+        } catch (\Exception $e) {
+            $this->errorMessage = $e->getMessage();
+            return false;
+        }
+    }
+
+    public function message()
+    {
+        return $this->errorMessage;
+    }
+}

laravel_app/resources/views/components/mosaic-create-modal.blade.php

@@ -0,0 +1,51 @@
+@props([
+    'formData',
+    /** @var \App\Livewire\Projects\MosaicManager */
+    'manager'
+])
+
+<x-modal wire:model.live="showCreateModal" {{ $attributes }} >
+    <x-form-modal submit="saveMosiac" wire:loading.class="opacity-50">
+        <x-slot name="title">
+            {{ __('Project') }}
+        </x-slot>
+
+        <x-slot name="description">
+            {{ __('Report generator for generating reports') }}
+        </x-slot>
+
+
+        <x-slot name="form">
+            <div class="col-span-6 sm:col-span-4">
+                <x-label for="year" value="{{ __('Year') }}"/>
+                <x-input id="year" type="text" class="mt-1 block w-full" wire:model.live="formData.year" autofocus/>
+                <x-input-error for="formData.year" class="mt-2"/>
+            </div><div class="col-span-6 sm:col-span-4">
+                <x-label for="week" value="{{ __('Week') }}"/>
+                <x-input id="week" type="text" class="mt-1 block w-full" wire:model.live="formData.week" autofocus/>
+                <x-input-error for="formData.week" class="mt-2"/>
+                <x-input-error for="formData" class="mt-2"/>
+            </div>
+            <div>
+                <span class="whitespace-nowrap">{!! $manager->dateRange !!}</span>
+            </div>
+        </x-slot>
+
+        <x-slot name="actions">
+            <x-action-message class="mr-3" on="saved">
+                {{ __('Saved.') }}
+            </x-action-message>
+
+            <x-secondary-button class="mr-3"
+                                type="button"
+                                x-on:click="$wire.showCreateModal = 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/mosaic-manager.blade.php

@@ -0,0 +1,52 @@
+<div>
+    <div class="px-4 sm:px-6 lg:px-8">
+        <div class="sm:flex sm:items-center">
+            <div class="sm:flex-auto">
+                <h1 class="text-base font-semibold leading-6 text-gray-900">Reports</h1>
+                <p class="mt-2 text-sm text-gray-700"></p>
+            </div>
+            <div class="mt-4 sm:ml-16 sm:mt-0 sm:flex-none">
+                <x-button wire:click="openCreateMosiacsModal"
+                          class="block rounded-md bg-indigo-600 px-3 py-2 text-center 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">
+                    Create Mosaic
+                </x-button>
+            </div>
+        </div>
+        <div class="mt-8 flow-root">
+            <div class="-mx-4 -my-2 overflow-x-auto sm:-mx-6 lg:-mx-8">
+                <div class="inline-block min-w-full py-2 align-middle">
+                    <table class="min-w-full divide-y divide-gray-300">
+                        <thead>
+                        <tr>
+                            <th scope="col"
+                                class="py-3.5 pl-4 pr-3 text-left text-sm font-semibold text-gray-900 sm:pl-6 lg:pl-8">
+                                Name
+                            </th>
+                            <th scope="col" class="px-3 py-3.5 text-left text-sm font-semibold text-gray-900">
+                                Status
+                            </th>
+                            <th scope="col" class="relative py-3.5 pl-3 pr-4 sm:pr-6 lg:pr-8">
+                                <span class="sr-only">Edit</span>
+                            </th>
+                        </tr>
+                        </thead>
+                        <tbody class="divide-y divide-gray-200 bg-white">
+                        @foreach($project->getMosaicList() as $mosaic)
+                            <tr>
+                            <td class="whitespace-nowrap py-4 pl-4 pr-3 text-sm font-medium text-gray-900 sm:pl-6 lg:pl-8">{{ $project->name }}</td>
+                            <td class="whitespace-nowrap px-3 py-4 text-sm text-gray-500">
+                            {{ $mosaic }}
+                            </td>
+                            <td class="relative whitespace-nowrap py-4 pl-3 pr-4 text-right text-sm font-medium sm:pr-6 lg:pr-8">
+
+                            </td>
+                            </tr>
+                        @endforeach
+                        </tbody>
+                    </table>
+                </div>
+            </div>
+        </div>
+    </div>
+    <x-mosaic-create-modal :manager="$this"/>
+</div>

laravel_app/resources/views/livewire/projects/report-manager.blade.php

@@ -1,6 +1,4 @@
 <div>
-
-
     <div class="px-4 sm:px-6 lg:px-8">
         <div class="sm:flex sm:items-center">
             <div class="sm:flex-auto">

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

@@ -12,6 +12,11 @@
                     :class="$tab.isSelected ? 'border-gray-200 bg-white' : 'border-transparent'"
                     class="inline-flex rounded-l-md border-t border-l border-b px-5 py-2.5"
             >{{ __('Downloads') }}</button>
+            <button x-tabs:tab type="button"
+                    data-tab-name="mosaics"
+                    :class="$tab.isSelected ? 'border-gray-200 bg-white' : 'border-transparent'"
+                    class="inline-flex rounded-l-md border-t border-l border-b px-5 py-2.5"
+            >{{ __('Mosaic') }}</button>
             <button x-tabs:tab type="button"
                     data-tab-name="mailing"
                     :class="$tab.isSelected ? 'border-gray-200 bg-white' : 'border-transparent'"
@@ -28,7 +33,9 @@ class="inline-flex rounded-l-md border-t border-l border-b px-5 py-2.5"
             <section x-tabs:panel class="p-8">
                 <livewire:projects.download-manager :project="$project" />
             </section>
-
+            <section x-tabs:panel class="p-8">
+                <livewire:projects.mosaic-manager :project="$project" />
+            </section>
             <section x-tabs:panel class="p-8">
                 <livewire:projects.mailing-manager :project="$project" />
             </section>

laravel_app/tests/Unit/Rules/AllMergedTiffsPresentRuleTest.php

@@ -0,0 +1,94 @@
+<?php
+
+namespace Tests\Unit\Rules;
+
+use App\Models\Project;
+
+use App\Rules\AllMergedTiffsPresentRule;
+use Illuminate\Foundation\Testing\RefreshDatabase;
+use Illuminate\Support\Carbon;
+use Mockery;
+use Tests\TestCase;
+
+class AllMergedTiffsPresentRuleTest extends TestCase
+{
+    use RefreshDatabase;
+
+    protected function setUp(): void
+    {
+        parent::setUp(); // TODO: Change the autogenerated stub
+    }
+
+    /**
+     * @test
+     */
+    public function validatesCorrectValue()
+    {
+        $project = Project::create([
+            'name'           => 'Test project',
+            'mail_template'  => 'Test mail template',
+            'mail_subject'   => 'Test mail subject',
+            'mail_frequency' => 'Test mail frequency',
+            'mail_day'       => 'Friday',
+            'download_path'  => 'test_project',
+        ]);
+
+        $projectMock = Mockery::mock($project)->makePartial();
+
+        $projectMock->shouldReceive('getMergedTiffList')->andReturn(
+            collect([
+                "chemba/merged_tiff/2021-01-04.tif",
+                "chemba/merged_tiff/2021-01-05.tif",
+                "chemba/merged_tiff/2021-01-06.tif",
+                "chemba/merged_tiff/2021-01-07.tif",
+                "chemba/merged_tiff/2021-01-08.tif",
+                "chemba/merged_tiff/2021-01-09.tif",
+                "chemba/merged_tiff/2021-01-10.tif",
+            ]));
+
+        $rule = new AllMergedTiffsPresentRule($projectMock);
+
+        $this->assertTrue($rule->passes(
+            'attribute',
+            ['year' => '2021', 'week' => '1']
+        ));
+    }
+
+    public function testInvalidatesIncorrectValue()
+    {
+        $project = Project::create([
+            'name'           => 'Test project',
+            'mail_template'  => 'Test mail template',
+            'mail_subject'   => 'Test mail subject',
+            'mail_frequency' => 'Test mail frequency',
+            'mail_day'       => 'Friday',
+            'download_path'  => 'test_project',
+        ]);
+
+        $projectMock = Mockery::mock($project)->makePartial();
+
+        $projectMock->shouldReceive('getMergedTiffList')->andReturn(
+            collect([
+//                "chemba/merged_tiff/2021-01-04.tif",
+                "chemba/merged_tiff/2021-01-05.tif",
+                "chemba/merged_tiff/2021-01-06.tif",
+                "chemba/merged_tiff/2021-01-07.tif",
+                "chemba/merged_tiff/2021-01-08.tif",
+                "chemba/merged_tiff/2021-01-09.tif",
+                "chemba/merged_tiff/2021-01-10.tif",
+            ]));
+
+
+        $rule = new AllMergedTiffsPresentRule($projectMock);
+
+        $this->assertFalse($rule->passes(
+            'attribute',
+            ['year' => '2021', 'week' => '1']
+        ));
+        $this->assertEquals(
+            'Missing merged tiffs: 2021-01-04',
+            $rule->message()
+        );
+    }
+
+}

python_app/Chemba_download.ipynb

@@ -335,6 +335,8 @@
     "  # Adjust the number of days needed\n",
     "\n",
     "end = datetime.date.today()\n",
+    "#end = datetime.datetime(2023, 11, 10)\n",
+    "#start = datetime.datetime(2023, 10, 19)\n",
     "start = end - datetime.timedelta(days=days_needed - 1)\n",
     "\n",
     "slots = [(start + datetime.timedelta(days=i)).strftime('%Y-%m-%d') for i in range(days_needed)]\n",

r_app/2_CI_data_prep.R

@@ -11,7 +11,21 @@ library(exactextractr)
 
 library(CIprep)
 
+# Vang alle command line argumenten op
+args <- commandArgs(trailingOnly = TRUE)
 
+# Controleer of er ten minste één argument is doorgegeven
+if (length(args) == 0) {
+  stop("Geen argumenten doorgegeven aan het script")
+}
+
+# Converteer het eerste argument naar een numerieke waarde
+weeks_ago <- as.numeric(args[1])
+
+# Controleer of weeks_ago een geldig getal is
+if (is.na(weeks_ago)) {
+  stop("Het argument is geen geldig getal")
+}
 
 laravel_storage_dir <- here("../laravel_app/storage/app")
 #preparing directories
@@ -38,13 +52,13 @@ dir.create(merged_final)
 
 
 # Creating weekly mosaic
-dates <- date_list(0)
+dates <- date_list(weeks_ago)
+head(dates)
+print(planet_tif_folder)
 
 #load pivot geojson
 pivot_sf_q <- st_read(here( "pivot_20210625.geojson")) %>% dplyr::select(pivot, pivot_quadrant) %>% vect()
 
-#load and filter raster files
-raster_files <- list.files(planet_tif_folder,full.names = T, pattern = ".tif") #use pattern = '.tif$' or something else if you have multiple files in this folder
 filtered_files  <- map(dates$days_filter, ~ raster_files[grepl(pattern = .x, x = raster_files)]) %>%
   compact() %>%
   flatten_chr()

r_app/CI_report_dashboard_planet.Rmd

@@ -2,6 +2,8 @@
 # title: paste0("CI report week ", week, " - all pivots from ", last_tuesday, " to ", today)
 params:
   ref: word-styles-reference-03.docx
+  output_file: "CI_report.docx"
+  report_date: "2023-12-12"
 output:
   word_document:
     reference_docx: !expr file.path("word-styles-reference-03.docx")
@@ -11,6 +13,12 @@ editor_options:
 ---
 
 ```{r setup, include=FALSE}
+#set de filename van de output
+knitr::opts_chunk$set(echo = TRUE)
+output_file <- params$output_file
+report_date <- params$report_date
+
+
 # Activeer de renv omgeving
 renv::activate()
 
@@ -50,12 +58,13 @@ s2_dir <- "C:/Users/timon/Resilience BV/4002 CMD App - General/4002 CMD Team/400
 
 ```{r week, message=FALSE, warning=FALSE, include=FALSE}
 # week <- 5
-# today = "2023-10-08"
+#today = "2023-12-12"
-# week <- week(today)
+today <- as.character(report_date)
+week <- week(today)
  #today = "2022-08-18"
 
-today = as.character(Sys.Date())
+#today = as.character(Sys.Date())
-week = lubridate::week(Sys.time())
+#week = lubridate::week(Sys.time())
 ## week = 26
 title_var <- paste0("CI dashboard week ", week, " - all pivots dashboard using 3x3 meter resolution")
 ```
@@ -97,7 +106,6 @@ last_week_dif_raster <- ((CI - CI_m1) / CI_m1) * 100
 last_week_dif_raster_abs <- (CI - CI_m1)
 two_week_dif_raster_abs <- (CI - CI_m2)
 
-
 AllPivots0 <-st_read(here(data_dir, "pivot_20210625.geojson"))
 joined_spans <-st_read(here(data_dir, "spans2.geojson")) %>% st_transform(crs(AllPivots0))
 

renv/.gitignore

@@ -0,0 +1,7 @@
+library/
+local/
+cellar/
+lock/
+python/
+sandbox/
+staging/

runcane.sh

@@ -1,4 +1,7 @@
 #!/bin/bash
+
+output_file=${1:-"standaard_naam.html"}
+ref=${2:-"word-styles-reference-03.docx"}
 # Directory waar de virtuele omgeving zal worden aangemaakt
 #VENV_DIR="./python_app/myenv"
 
@@ -18,5 +21,6 @@ Rscript 2_CI_data_prep.R
 #
 ## Runnen van Rmd bestand
 # -e betekent "evalueren" en -i specificeert de input file
-Rscript -e "rmarkdown::render('CI_report_dashboard_planet.Rmd', 'all')"
+#Rscript -e "rmarkdown::render('CI_report_dashboard_planet.Rmd', 'all')"
+Rscript -e "rmarkdown::render('CI_report_dashboard_planet.Rmd', output_file='$output_file', params=list(ref='$ref'))"
 cd ..

runpython.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # Standaardwaarde voor days
-days=28
+days=7
 
 # Loop door alle argumenten
 for arg in "$@"