feat(geo): extract country from geo locations and add world map

app/Console/Commands/EnrichGeoLocations.php

@@ -0,0 +1,115 @@
+<?php
+
+namespace App\Console\Commands;
+
+use App\Models\GeoLocation;
+use App\Services\GeoLocationEnricher;
+use Illuminate\Console\Command;
+
+class EnrichGeoLocations extends Command
+{
+    protected $signature = 'coconut:enrich-geo-locations
+                            {--dry-run : Report only, no writes}
+                            {--rules-only : Skip Nominatim geocoding}
+                            {--geocode-only : Only geocode rows missing country_code}
+                            {--force : Re-enrich even if country_code is set}
+                            {--limit= : Cap rows processed (for testing)}';
+
+    protected $description = 'Extract country metadata from geo location names using rules and Nominatim geocoding';
+
+    public function handle(GeoLocationEnricher $enricher): int
+    {
+        $dryRun = (bool) $this->option('dry-run');
+        $rulesOnly = (bool) $this->option('rules-only');
+        $geocodeOnly = (bool) $this->option('geocode-only');
+        $force = (bool) $this->option('force');
+        $limit = $this->option('limit') !== null ? (int) $this->option('limit') : null;
+
+        $query = GeoLocation::query()->orderBy('id');
+
+        if (! $force) {
+            $query->whereNull('country_code');
+        }
+
+        if ($limit !== null) {
+            $query->limit($limit);
+        }
+
+        $records = $query->get();
+        $total = $records->count();
+
+        if ($total === 0) {
+            $this->info('No geo locations to process.');
+
+            return self::SUCCESS;
+        }
+
+        $this->info("Processing {$total} geo location(s)...");
+
+        $stats = [
+            'segment' => 0,
+            'whole' => 0,
+            'parens_mx' => 0,
+            'substring' => 0,
+            'geocoded' => 0,
+            'failed' => 0,
+            'skipped' => 0,
+        ];
+
+        $allowGeocoding = ! $rulesOnly;
+
+        $bar = $this->output->createProgressBar($total);
+        $bar->start();
+
+        foreach ($records as $geoLocation) {
+            if (! $force && filled($geoLocation->country_code)) {
+                $stats['skipped']++;
+                $bar->advance();
+
+                continue;
+            }
+
+            if ($dryRun) {
+                $result = $enricher->resolve(
+                    $geoLocation->name,
+                    allowGeocoding: $allowGeocoding,
+                    geocodeOnly: $geocodeOnly,
+                );
+            } else {
+                $result = $enricher->enrich(
+                    $geoLocation,
+                    allowGeocoding: $allowGeocoding,
+                    force: $force,
+                    geocodeOnly: $geocodeOnly,
+                );
+            }
+
+            if ($result !== null) {
+                $method = $result->method === 'geocoded' ? 'geocoded' : $result->method;
+                $stats[$method] = ($stats[$method] ?? 0) + 1;
+            } else {
+                $stats['failed']++;
+            }
+
+            $bar->advance();
+        }
+
+        $bar->finish();
+        $this->newLine(2);
+
+        $matched = $stats['segment'] + $stats['whole'] + $stats['parens_mx'] + $stats['substring'] + $stats['geocoded'];
+
+        $this->table(
+            ['Method', 'Count'],
+            collect($stats)->map(fn (int $count, string $method) => [$method, $count])->values()->all(),
+        );
+
+        $this->info("Matched: {$matched} / {$total}");
+
+        if ($dryRun) {
+            $this->warn('Dry run only — no records were updated.');
+        }
+
+        return self::SUCCESS;
+    }
+}

app/Console/Commands/ImportOrganismMetadata.php

@@ -3,6 +3,7 @@
 namespace App\Console\Commands;
 
 use App\Models\Entry;
+use App\Services\GeoLocationService;
 use Illuminate\Console\Command;
 use Illuminate\Database\QueryException;
 use Illuminate\Support\Facades\DB;
@@ -1300,45 +1301,11 @@ protected function findOrCreateGeoLocation(string $name): ?int
             return null;
         }
 
-        if (isset($this->geoLocationCache[$name])) {
-            return $this->geoLocationCache[$name];
-        }
-
-        $existing = DB::selectOne('SELECT id FROM geo_locations WHERE name = ?', [$name]);
-        if ($existing) {
-            $this->geoLocationCache[$name] = $existing->id;
-
-            return $existing->id;
-        }
-
-        try {
-            $id = DB::table('geo_locations')->insertGetId([
-                'name' => $name,
-                'created_at' => now(),
-                'updated_at' => now(),
-            ]);
-            $this->geoLocationCache[$name] = $id;
-
-            return $id;
-        } catch (QueryException $e) {
-            if (! $this->isUniqueViolation($e)) {
-                Log::error('Unexpected DB error in geo_locations insert (not unique violation)', [
-                    'sqlstate' => $e->errorInfo[0] ?? null,
-                    'msg' => $e->getMessage(),
-                ]);
-                throw $e;
-            }
-
-            // Handle race condition - unique violation
-            usleep(50000);
-            $existing = DB::selectOne('SELECT id FROM geo_locations WHERE name = ?', [$name]);
-            if ($existing) {
-                $this->geoLocationCache[$name] = $existing->id;
-
-                return $existing->id;
-            }
-            throw $e;
-        }
+        return app(GeoLocationService::class)->findOrCreateId(
+            $name,
+            $this->geoLocationCache,
+            allowGeocoding: false,
+        );
     }
 
     protected function findOrCreateEcosystem(string $name, ?int $geoLocationId = null): ?int

app/Console/Commands/SubmissionsAutoProcess/ImportEntriesReferencesAuto.php

@@ -2,6 +2,7 @@
 
 namespace App\Console\Commands\SubmissionsAutoProcess;
 
+use App\Services\GeoLocationService;
 use Illuminate\Console\Command;
 use Illuminate\Database\QueryException;
 use Illuminate\Support\Facades\DB;
@@ -1110,36 +1111,11 @@ protected function findOrCreateGeoLocation(string $name): ?int
             return null;
         }
 
-        if (isset($this->geoLocationCache[$name])) {
-            return $this->geoLocationCache[$name];
-        }
-
-        $existing = DB::selectOne('SELECT id FROM geo_locations WHERE name = ?', [$name]);
-        if ($existing) {
-            $this->geoLocationCache[$name] = $existing->id;
-
-            return $existing->id;
-        }
-
-        try {
-            $id = DB::table('geo_locations')->insertGetId([
-                'name' => $name,
-                'created_at' => now(),
-                'updated_at' => now(),
-            ]);
-            $this->geoLocationCache[$name] = $id;
-
-            return $id;
-        } catch (QueryException $e) {
-            usleep(50000);
-            $existing = DB::selectOne('SELECT id FROM geo_locations WHERE name = ?', [$name]);
-            if ($existing) {
-                $this->geoLocationCache[$name] = $existing->id;
-
-                return $existing->id;
-            }
-            throw $e;
-        }
+        return app(GeoLocationService::class)->findOrCreateId(
+            $name,
+            $this->geoLocationCache,
+            allowGeocoding: false,
+        );
     }
 
     protected function findOrCreateEcosystem(string $name, ?int $geoLocationId = null): ?int

app/Filament/Dashboard/Resources/ReportResource.php

@@ -24,6 +24,7 @@
 use App\Models\Report;
 use App\Models\ReportUser;
 use App\Models\User;
+use App\Services\GeoLocationService;
 use Closure;
 use Filament\Actions\Action;
 use Filament\Actions\BulkActionGroup;
@@ -1658,7 +1659,7 @@ public static function runSQLQueries(Report $record): void
                 if (! empty(self::$overall_changes['geo_location_changes']['add'])) {
                     $geoLocations = explode(',', self::$overall_changes['geo_location_changes']['add']);
                     foreach ($geoLocations as $newLocation) {
-                        $geo_location = GeoLocation::firstOrCreate(['name' => $newLocation]);
+                        $geo_location = app(GeoLocationService::class)->findOrCreate(trim($newLocation));
                         $molecule->auditAttach('geo_locations', $geo_location);
                     }
                 }

app/Jobs/ImportEntry.php

@@ -3,9 +3,9 @@
 namespace App\Jobs;
 
 use App\Models\Citation;
-use App\Models\GeoLocation;
 use App\Models\Molecule;
 use App\Models\Organism;
+use App\Services\GeoLocationService;
 use Exception;
 use Illuminate\Bus\Batchable;
 use Illuminate\Bus\Queueable;
@@ -236,7 +236,7 @@ public function saveGeoLocationDetails($geo_location, $molecule)
         $locations = explode('|', $this->entry->locations);
         $i = 0;
         foreach ($geo_locations as $geo_location) {
-            $geolocationModel = GeoLocation::firstOrCreate(['name' => $geo_location]);
+            $geolocationModel = app(GeoLocationService::class)->findOrCreate($geo_location, allowGeocoding: false);
             $locationsNames = array_key_exists($i, $locations) ? $locations[$i] : '';
             $molecule->geo_locations()->syncWithoutDetaching([$geolocationModel->id => ['locations' => $locationsNames]]);
             $i = $i + 1;

app/Jobs/ImportEntryAuto.php

@@ -4,11 +4,11 @@
 
 use App\Models\Citation;
 use App\Models\Ecosystem;
-use App\Models\GeoLocation;
 use App\Models\Molecule;
 use App\Models\MoleculeOrganism;
 use App\Models\Organism;
 use App\Models\SampleLocation;
+use App\Services\GeoLocationService;
 use Exception;
 use Illuminate\Bus\Batchable;
 use Illuminate\Bus\Queueable;
@@ -253,9 +253,10 @@ public function saveOrganismDetails($organisms, $molecule)
                 foreach ($organism['locations'] as $location) {
                     $geo_location_ids = []; // Reset for each location
 
-                    $geoLocationModel = GeoLocation::firstOrCreate([
-                        'name' => $location['name'],
-                    ]);
+                    $geoLocationModel = app(GeoLocationService::class)->findOrCreate(
+                        $location['name'],
+                        allowGeocoding: false,
+                    );
 
                     // Connect organism to geo location directly
                     // $organismModel->geoLocations()->syncWithoutDetaching([$geoLocationModel->id]);

app/Livewire/GeoGlobe.php

@@ -0,0 +1,28 @@
+<?php
+
+namespace App\Livewire;
+
+use App\Services\GeoLocationGlobeStatsService;
+use Livewire\Attributes\Layout;
+use Livewire\Component;
+
+#[Layout('layouts.guest')]
+class GeoGlobe extends Component
+{
+    public array $countryStats = [];
+
+    public array $totals = [];
+
+    public function mount(GeoLocationGlobeStatsService $statsService): void
+    {
+        $data = $statsService->getCountryStats();
+
+        $this->countryStats = $data['countries'];
+        $this->totals = $data['totals'];
+    }
+
+    public function render()
+    {
+        return view('livewire.geo-globe');
+    }
+}