Feat/app/create mycobank id updater

app/Console/Commands/RegisterFungiOccurences.php

@@ -109,7 +109,7 @@ private function fetchIUCNData(string $genus, string $species): int
             return RedListClassification::NA->value;
         }
     }
-  
+
     private function buildFungiData(array $row): array
     {
         return [

app/Console/Kernel.php

@@ -2,6 +2,7 @@
 
 namespace App\Console;
 
+use App\Jobs\UpdateTaxonomyFromMycoBank;
 use Illuminate\Console\Scheduling\Schedule;
 use Illuminate\Foundation\Console\Kernel as ConsoleKernel;
 
@@ -12,7 +13,7 @@ class Kernel extends ConsoleKernel
      */
     protected function schedule(Schedule $schedule): void
     {
-        // $schedule->command('inspire')->hourly();
+        $schedule->job(UpdateTaxonomyFromMycoBank::class)->monthlyOn(1);
     }
 
     /**

app/Jobs/UpdateTaxonomyFromMycoBank.php

@@ -0,0 +1,92 @@
+<?php
+
+namespace App\Jobs;
+
+use App\Models\Taxonomy;
+use App\Services\Platforms\MycoBank\MycoBank;
+use Box\Spout\Reader\Common\Creator\ReaderEntityFactory;
+use Illuminate\Bus\Queueable;
+use Illuminate\Contracts\Queue\ShouldQueue;
+use Illuminate\Foundation\Bus\Dispatchable;
+use Illuminate\Queue\InteractsWithQueue;
+use Illuminate\Queue\SerializesModels;
+use Illuminate\Support\Facades\Log;
+
+class UpdateTaxonomyFromMycoBank implements ShouldQueue
+{
+    use Dispatchable, InteractsWithQueue, Queueable, SerializesModels;
+
+    public function handle(MycoBank $service): void
+    {
+        $filepath = $service->downloadFungiList();
+
+        $reader = ReaderEntityFactory::createXLSXReader();
+
+        try {
+            $reader->open($filepath);
+            $localTaxa = $this->getLocalTaxonomies();
+
+            foreach ($reader->getSheetIterator() as $sheet) {
+                $header = null;
+
+                foreach ($sheet->getRowIterator() as $rowIndex => $row) {
+                    $cells = $row->toArray();
+
+                    // Map header columns on first row
+                    if ($rowIndex === 1) {
+                        $header = array_flip($cells);
+                        continue;
+                    }
+
+                    if (!$header || !isset($header['Taxon name'])) {
+                        Log::warning('Invalid sheet format: missing "Taxon name" column.');
+                        break;
+                    }
+
+                    $taxonName = trim($cells[$header['Taxon name']] ?? '');
+                    if ($taxonName === '') {
+                        continue;
+                    }
+
+                    $fungi = $localTaxa[$taxonName] ?? null;
+                    if (!$fungi) {
+                        continue;
+                    }
+
+                    $this->updateFungiRecord($fungi, $cells, $header);
+                }
+            }
+        } catch (\Throwable $e) {
+            Log::error('MycoBank import failed: ' . $e->getMessage(), ['trace' => $e->getTraceAsString()]);
+        } finally {
+            $reader->close();
+        }
+    }
+    private function getLocalTaxonomies(): array
+    {
+        return Taxonomy::all()
+            ->mapWithKeys(fn($t) => [$t->genus . ' ' . $t->specie => $t])
+            ->toArray();
+    }
+
+    private function updateFungiRecord(array $fungiData, array $cells, array $header): void
+    {
+        $fungi = Taxonomy::find($fungiData['id']);
+        $mycoBankId = $cells[$header['MycoBank #']] ?? null;
+
+        $updates = [];
+
+        if (!$fungi) {
+            Log::warning("Taxonomy not found for ID: {$fungiData['id']}");
+            return;
+        }
+
+        if ($mycoBankId && $mycoBankId !== $fungi->external_id) {
+            $updates['external_id'] = $mycoBankId;
+        }
+
+        if (!empty($updates)) {
+            $fungi->fill($updates)->save();
+        }
+    }
+}

app/Services/Platforms/MycoBank/MycoBank.php

@@ -0,0 +1,78 @@
+<?php
+
+declare(strict_types=1);
+
+namespace App\Services\Platforms\MycoBank;
+
+use Exception;
+use GuzzleHttp\Client;
+use Illuminate\Support\Facades\Http;
+use Illuminate\Support\Facades\Storage;
+use PhpOffice\PhpSpreadsheet\IOFactory;
+use PhpOffice\PhpSpreadsheet\Spreadsheet;
+use Shuchkin\SimpleXLSX;
+use ZipArchive;
+
+class MycoBank
+{
+    public function __construct(protected ZipArchive $zipArchive) {}
+
+    public function downloadFungiList(): string
+    {
+        $name = storage_path('app/MycoBank/fungi_list_' . date('Y_m_d_H_i') . '.zip');
+
+        $client = new Client();
+        $client->get('https://www.mycobank.org/Images/MBList.zip', [
+            'sink' => $name
+        ]);
+
+        return $this->extractXlsxFromZip($name);
+    }
+
+    public function extractXlsxFromZip($zipPath)
+    {
+        $destinationPath = str_replace('.zip', '', $zipPath);
+        if (!file_exists($destinationPath)) {
+            mkdir($destinationPath, 0777, true);
+        }
+
+        $zip = new \ZipArchive;
+        if ($zip->open($zipPath) === true) {
+            $tempPath = storage_path('app/temp_unzip_' . uniqid());
+            mkdir($tempPath, 7777, true);
+
+            $zip->extractTo($tempPath);
+            $zip->close();
+
+            $xlsxFile = collect(scandir($tempPath))
+                ->first(fn($file) => str_ends_with($file, '.xlsx'));
+
+            if ($xlsxFile) {
+                $xlsxSource = $tempPath . '/' . $xlsxFile;
+                $xlsxTarget = $destinationPath . '/' . $xlsxFile;
+
+                rename($xlsxSource, $xlsxTarget);
+                $this->deleteDirectory($tempPath);
+
+                return $xlsxTarget;
+            } else {
+                $this->deleteDirectory($tempPath);
+                throw new \Exception("Nenhum arquivo XLSX encontrado no zip.");
+            }
+        } else {
+            throw new \Exception("Não foi possível abrir o arquivo ZIP.");
+        }
+    }
+
+    private function deleteDirectory($dir)
+    {
+        if (!file_exists($dir)) return true;
+        if (!is_dir($dir)) return unlink($dir);
+
+        foreach (scandir($dir) as $item) {
+            if ($item == '.' || $item == '..') continue;
+            $this->deleteDirectory($dir . DIRECTORY_SEPARATOR . $item);
+        }
+        return rmdir($dir);
+    }
+}

composer.json

@@ -2,15 +2,20 @@
     "name": "laravel/laravel",
     "type": "project",
     "description": "The skeleton application for the Laravel framework.",
-    "keywords": ["laravel", "framework"],
+    "keywords": [
+        "laravel",
+        "framework"
+    ],
     "license": "MIT",
     "require": {
         "php": "^8.1",
+        "box/spout": "^3.3",
         "guzzlehttp/guzzle": "^7.2",
         "laravel/framework": "^10.10",
         "laravel/sanctum": "^3.3",
         "laravel/tinker": "^2.8",
-        "phpoffice/phpspreadsheet": "^2.0",
+        "phpoffice/phpspreadsheet": "^5.1",
+        "shuchkin/simplexlsx": "^1.1",
         "tymon/jwt-auth": "^2.1"
     },
     "require-dev": {