Merge branch 'development' of https://github.com/Steinbeck-Lab/coconut …

…into development
Steinbeck-Lab · Jan 15, 2025 · 78e604c · 78e604c
2 parents a9140c8 + d87ed63
commit 78e604c
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Showing 18 changed files with 83 additions and 40 deletions.
diff --git a/app/Console/Commands/DashWidgetsRefresh.php b/app/Console/Commands/DashWidgetsRefresh.php
@@ -32,49 +32,49 @@ public function handle()
         // Cache::flush();
 
         // Create the cache for all DashboardStats widgets
-        Cache::rememberForever('stats.collections', function () {
+        Cache::flexible('stats.collections', [172800, 259200], function () {
             return DB::table('collections')->selectRaw('count(*)')->get()[0]->count;
         });
         $this->info('Cache for collections refreshed.');
 
-        Cache::rememberForever('stats.citations', function () {
+        Cache::flexible('stats.citations', [172800, 259200], function () {
             return DB::table('citations')->selectRaw('count(*)')->get()[0]->count;
         });
         $this->info('Cache for citations refreshed.');
 
-        Cache::rememberForever('stats.organisms', function () {
+        Cache::flexible('stats.organisms', [172800, 259200], function () {
             return DB::table('organisms')->selectRaw('count(*)')->get()[0]->count;
         });
         $this->info('Cache for organisms refreshed.');
 
-        Cache::rememberForever('stats.geo_locations', function () {
+        Cache::flexible('stats.geo_locations', [172800, 259200], function () {
             return DB::table('geo_locations')->selectRaw('count(*)')->get()[0]->count;
         });
         $this->info('Cache for geo locations refreshed.');
 
-        Cache::rememberForever('stats.reports', function () {
+        Cache::flexible('stats.reports', [172800, 259200], function () {
             return DB::table('reports')->selectRaw('count(*)')->get()[0]->count;
         });
         $this->info('Cache for reports refreshed.');
 
         // Create the cache for all DashboardStatsMid widgets
 
-        Cache::rememberForever('stats.molecules.non_stereo', function () {
+        Cache::flexible('stats.molecules.non_stereo', [172800, 259200], function () {
             return DB::table('molecules')->selectRaw('count(*)')->whereRaw('has_stereo=false and is_parent=false')->get()[0]->count;
         });
         $this->info('Cache for molecules non-stereo refreshed.');
 
-        Cache::rememberForever('stats.molecules.stereo', function () {
+        Cache::flexible('stats.molecules.stereo', [172800, 259200], function () {
             return DB::table('molecules')->selectRaw('count(*)')->whereRaw('has_stereo=true')->get()[0]->count;
         });
         $this->info('Cache for molecules stereo refreshed.');
 
-        Cache::rememberForever('stats.molecules.parent', function () {
+        Cache::flexible('stats.molecules.parent', [172800, 259200], function () {
             return DB::table('molecules')->selectRaw('count(*)')->whereRaw('has_stereo=false and is_parent=true')->get()[0]->count;
         });
         $this->info('Cache for molecules parent refreshed.');
 
-        Cache::rememberForever('stats.molecules', function () {
+        Cache::flexible('stats.molecules', [172800, 259200], function () {
             return DB::table('molecules')->selectRaw('count(*)')->whereRaw('active=true and NOT (is_parent=true AND has_variants=true)')->get()[0]->count;
         });
         $this->info('Cache for molecules refreshed.');

diff --git a/app/Filament/Dashboard/Resources/CitationResource.php b/app/Filament/Dashboard/Resources/CitationResource.php
@@ -12,6 +12,7 @@
 use Filament\Tables\Columns\TextColumn;
 use Filament\Tables\Table;
 use Illuminate\Support\Facades\Cache;
+use Illuminate\Support\Facades\DB;
 use Tapp\FilamentAuditing\RelationManagers\AuditsRelationManager;
 
 class CitationResource extends Resource
@@ -76,6 +77,8 @@ public static function getPages(): array
 
     public static function getNavigationBadge(): ?string
     {
-        return Cache::get('stats.citations');
+        return Cache::flexible('stats.citations', [172800, 259200], function () {
+            return DB::table('citations')->selectRaw('count(*)')->get()[0]->count;
+        });
     }
 }
diff --git a/app/Filament/Dashboard/Resources/CollectionResource.php b/app/Filament/Dashboard/Resources/CollectionResource.php
@@ -24,6 +24,7 @@
 use Filament\Tables\Table;
 use Illuminate\Database\Eloquent\Model;
 use Illuminate\Support\Facades\Cache;
+use Illuminate\Support\Facades\DB;
 use Illuminate\Support\Str;
 use Tapp\FilamentAuditing\RelationManagers\AuditsRelationManager;
 
@@ -161,6 +162,8 @@ public static function getWidgets(): array
 
     public static function getNavigationBadge(): ?string
     {
-        return Cache::get('stats.collections');
+        return Cache::flexible('stats.collections', [172800, 259200], function () {
+            return DB::table('collections')->selectRaw('count(*)')->get()[0]->count;
+        });
     }
 }
diff --git a/app/Filament/Dashboard/Resources/GeoLocationResource.php b/app/Filament/Dashboard/Resources/GeoLocationResource.php
@@ -10,6 +10,7 @@
 use Filament\Tables;
 use Filament\Tables\Table;
 use Illuminate\Support\Facades\Cache;
+use Illuminate\Support\Facades\DB;
 use Tapp\FilamentAuditing\RelationManagers\AuditsRelationManager;
 
 class GeoLocationResource extends Resource
@@ -83,6 +84,8 @@ public static function getWidgets(): array
 
     public static function getNavigationBadge(): ?string
     {
-        return Cache::get('stats.geo_locations');
+        return Cache::flexible('stats.geo_locations', [172800, 259200], function () {
+            return DB::table('geo_locations')->selectRaw('count(*)')->get()[0]->count;
+        });
     }
 }
diff --git a/app/Filament/Dashboard/Resources/GeoLocationResource/Widgets/GeoLocationStats.php b/app/Filament/Dashboard/Resources/GeoLocationResource/Widgets/GeoLocationStats.php
@@ -15,10 +15,10 @@ class GeoLocationStats extends BaseWidget
     protected function getStats(): array
     {
         return [
-            Stat::make('Total Molecules', Cache::rememberForever('stats.geo_locations'.$this->record->id.'molecules.count', function () {
+            Stat::make('Total Molecules', Cache::flexible('stats.geo_locations'.$this->record->id.'molecules.count', [172800, 259200], function () {
                 return DB::table('geo_location_molecule')->selectRaw('count(*)')->whereRaw('geo_location_id='.$this->record->id)->get()[0]->count;
             })),
-            Stat::make('Total Organisms', Cache::rememberForever('stats.geo_locations'.$this->record->id.'organisms.count', function () {
+            Stat::make('Total Organisms', Cache::flexible('stats.geo_locations'.$this->record->id.'organisms.count', [172800, 259200], function () {
                 return DB::table('geo_location_molecule')->selectRaw('count(*)')->whereRaw('geo_location_id='.$this->record->id)->Join('molecule_organism', 'geo_location_molecule.molecule_id', '=', 'molecule_organism.molecule_id')->get()[0]->count;
             })),
         ];

diff --git a/app/Filament/Dashboard/Resources/MoleculeResource.php b/app/Filament/Dashboard/Resources/MoleculeResource.php
@@ -14,7 +14,6 @@
 use App\Filament\Dashboard\Resources\MoleculeResource\Widgets\MoleculeStats;
 use App\Models\Molecule;
 use Archilex\AdvancedTables\Filters\AdvancedFilter;
-use DB;
 use Filament\Forms\Components\Select;
 use Filament\Forms\Components\Textarea;
 use Filament\Forms\Components\TextInput;
@@ -30,6 +29,7 @@
 use Illuminate\Database\Eloquent\Builder;
 use Illuminate\Database\Eloquent\Collection;
 use Illuminate\Support\Facades\Cache;
+use Illuminate\Support\Facades\DB;
 use Illuminate\Support\Facades\Redirect;
 use Illuminate\Support\HtmlString;
 use pxlrbt\FilamentExcel\Actions\Tables\ExportBulkAction;
@@ -249,7 +249,9 @@ public static function getWidgets(): array
 
     public static function getNavigationBadge(): ?string
     {
-        return Cache::get('stats.molecules');
+        return Cache::flexible('stats.molecules', [172800, 259200], function () {
+            return DB::table('molecules')->selectRaw('count(*)')->whereRaw('active=true and NOT (is_parent=true AND has_variants=true)')->get()[0]->count;
+        });
     }
 
     public static function changeMoleculeStatus($record, $reason)

diff --git a/app/Filament/Dashboard/Resources/MoleculeResource/Widgets/MoleculeStats.php b/app/Filament/Dashboard/Resources/MoleculeResource/Widgets/MoleculeStats.php
@@ -15,10 +15,10 @@ class MoleculeStats extends BaseWidget
     protected function getStats(): array
     {
         return [
-            Stat::make('Total Organisms', Cache::remember('stats.molecules'.$this->record->id.'organisms.count', 172800, function () {
+            Stat::make('Total Organisms', Cache::flexible('stats.molecules'.$this->record->id.'organisms.count', [172800, 259200], function () {
                 return DB::table('molecule_organism')->selectRaw('count(*)')->whereRaw('molecule_id='.$this->record->id)->get()[0]->count;
             })),
-            Stat::make('Total Geo Locations', Cache::remember('stats.molecules'.$this->record->id.'geo_locations.count', 172800, function () {
+            Stat::make('Total Geo Locations', Cache::flexible('stats.molecules'.$this->record->id.'geo_locations.count', [172800, 259200], function () {
                 return DB::table('geo_location_molecule')->selectRaw('count(*)')->whereRaw('molecule_id='.$this->record->id)->get()[0]->count;
             })),
         ];

diff --git a/app/Filament/Dashboard/Resources/OrganismResource.php b/app/Filament/Dashboard/Resources/OrganismResource.php
@@ -19,6 +19,7 @@
 use GuzzleHttp\Client;
 use Illuminate\Contracts\View\View;
 use Illuminate\Support\Facades\Cache;
+use Illuminate\Support\Facades\DB;
 use Log;
 use Tapp\FilamentAuditing\RelationManagers\AuditsRelationManager;
 
@@ -130,7 +131,9 @@ public static function getWidgets(): array
 
     public static function getNavigationBadge(): ?string
     {
-        return Cache::get('stats.organisms');
+        return Cache::flexible('stats.organisms', [172800, 259200], function () {
+            return DB::table('organisms')->selectRaw('count(*)')->get()[0]->count;
+        });
     }
 
     protected static function getGNFMatches($name, $organism)

diff --git a/app/Filament/Dashboard/Resources/OrganismResource/Widgets/OrganismStats.php b/app/Filament/Dashboard/Resources/OrganismResource/Widgets/OrganismStats.php
@@ -15,10 +15,10 @@ class OrganismStats extends BaseWidget
     protected function getStats(): array
     {
         return [
-            Stat::make('Total Molecules', Cache::remember('stats.organisms'.$this->record->id.'molecules.count', 172800, function () {
+            Stat::make('Total Molecules', Cache::flexible('stats.organisms'.$this->record->id.'molecules.count', [172800, 259200], function () {
                 return DB::table('molecule_organism')->selectRaw('count(*)')->whereRaw('organism_id='.$this->record->id)->get()[0]->count;
             })),
-            Stat::make('Total Geo Locations', Cache::remember('stats.organisms'.$this->record->id.'geo_locations.count', 172800, function () {
+            Stat::make('Total Geo Locations', Cache::flexible('stats.organisms'.$this->record->id.'geo_locations.count', [172800, 259200], function () {
                 return DB::table('molecule_organism')->selectRaw('count(*)')->whereRaw('organism_id='.$this->record->id)->Join('geo_location_molecule', 'molecule_organism.molecule_id', '=', 'geo_location_molecule.molecule_id')->get()[0]->count;
             })),
         ];

diff --git a/app/Filament/Dashboard/Widgets/DashboardStats.php b/app/Filament/Dashboard/Widgets/DashboardStats.php
@@ -5,6 +5,7 @@
 use Filament\Widgets\StatsOverviewWidget as BaseWidget;
 use Filament\Widgets\StatsOverviewWidget\Stat;
 use Illuminate\Support\Facades\Cache;
+use Illuminate\Support\Facades\DB;
 
 class DashboardStats extends BaseWidget
 {
@@ -18,12 +19,22 @@ public function getColumns(): int
     protected function getStats(): array
     {
         return [
-            Stat::make('Total Collections', Cache::get('stats.collections')),
-            Stat::make('Total Citations', Cache::get('stats.citations')),
+            Stat::make('Total Collections', Cache::flexible('stats.collections', [172800, 259200], function () {
+                return DB::table('collections')->selectRaw('count(*)')->get()[0]->count;
+            })),
+            Stat::make('Total Citations', Cache::flexible('stats.citations', [172800, 259200], function () {
+                return DB::table('citations')->selectRaw('count(*)')->get()[0]->count;
+            })),
 
-            Stat::make('Total Organisms', Cache::get('stats.organisms')),
-            Stat::make('Total Geo Locations', Cache::get('stats.geo_locations')),
-            Stat::make('Total Reports', Cache::get('stats.reports')),
+            Stat::make('Total Organisms', Cache::flexible('stats.organisms', [172800, 259200], function () {
+                return DB::table('organisms')->selectRaw('count(*)')->get()[0]->count;
+            })),
+            Stat::make('Total Geo Locations', Cache::flexible('stats.geo_locations', [172800, 259200], function () {
+                return DB::table('geo_locations')->selectRaw('count(*)')->get()[0]->count;
+            })),
+            Stat::make('Total Reports', Cache::flexible('stats.reports', [172800, 259200], function () {
+                return DB::table('reports')->selectRaw('count(*)')->get()[0]->count;
+            })),
         ];
     }
 }
diff --git a/app/Filament/Dashboard/Widgets/DashboardStatsMid.php b/app/Filament/Dashboard/Widgets/DashboardStatsMid.php
@@ -5,6 +5,7 @@
 use Filament\Widgets\StatsOverviewWidget as BaseWidget;
 use Filament\Widgets\StatsOverviewWidget\Stat;
 use Illuminate\Support\Facades\Cache;
+use Illuminate\Support\Facades\DB;
 
 class DashboardStatsMid extends BaseWidget
 {
@@ -15,11 +16,19 @@ class DashboardStatsMid extends BaseWidget
     protected function getStats(): array
     {
         return [
-            Stat::make('Total Molecules', Cache::get('stats.molecules')),
-            Stat::make('Total Non-Stereo Molecules', Cache::get('stats.molecules.non_stereo')),
-            Stat::make('Total Stereo Molecules', Cache::get('stats.molecules.stereo'))
+            Stat::make('Total Molecules', Cache::flexible('stats.molecules', [172800, 259200], function () {
+                return DB::table('molecules')->selectRaw('count(*)')->whereRaw('active=true and NOT (is_parent=true AND has_variants=true)')->get()[0]->count;
+            })),
+            Stat::make('Total Non-Stereo Molecules', Cache::flexible('stats.molecules.non_stereo', [172800, 259200], function () {
+                return DB::table('molecules')->selectRaw('count(*)')->whereRaw('has_stereo=false and is_parent=false')->get()[0]->count;
+            })),
+            Stat::make('Total Stereo Molecules', Cache::flexible('stats.molecules.stereo', [172800, 259200], function () {
+                return DB::table('molecules')->selectRaw('count(*)')->whereRaw('has_stereo=true')->get()[0]->count;
+            }))
                 ->description(
-                    'Total parent molecules: '.Cache::get('stats.molecules.parent')
+                    'Total parent molecules: '.Cache::flexible('stats.molecules.parent', [172800, 259200], function () {
+                        return DB::table('molecules')->selectRaw('count(*)')->whereRaw('has_stereo=false and is_parent=true')->get()[0]->count;
+                    })
                 )
                 ->color('primary'),
         ];

diff --git a/app/Http/Controllers/API/Schemas/Bioschemas/MolecularEntityController.php b/app/Http/Controllers/API/Schemas/Bioschemas/MolecularEntityController.php
@@ -15,7 +15,7 @@ class MolecularEntityController extends Controller
 {
     public function moleculeSchema(Request $request, $identifier)
     {
-        $molecule = Cache::remember('molecules.'.$identifier, 172800, function () use ($identifier) {
+        $molecule = Cache::flexible('molecules.'.$identifier, [172800, 259200], function () use ($identifier) {
             return Molecule::where('identifier', $identifier)->first();
         });
 

diff --git a/app/Http/Controllers/CollectionController.php b/app/Http/Controllers/CollectionController.php
@@ -17,7 +17,7 @@ public function __invoke(Request $request, $id)
             abort(404);
         }
 
-        $collection = Cache::remember('collections.'.$id, 172800, function () use ($id) {
+        $collection = Cache::flexible('collections.'.$id, [172800, 259200], function () use ($id) {
             return Collection::where('identifier', $id)->first();
         });
 

diff --git a/app/Http/Controllers/MoleculeController.php b/app/Http/Controllers/MoleculeController.php
@@ -17,7 +17,7 @@ public function __invoke(Request $request, $id)
             $id .= '.0';
         }
 
-        $molecule = Cache::remember('molecules.'.$id, 172800, function () use ($id) {
+        $molecule = Cache::flexible('molecules.'.$id, [172800, 259200], function () use ($id) {
             return Molecule::where('identifier', $id)->first();
         });
 

diff --git a/app/Livewire/DataSources.php b/app/Livewire/DataSources.php
@@ -12,7 +12,7 @@ class DataSources extends Component
 
     public function mount()
     {
-        $this->collections = Cache::remember('collections', 172800, function () {
+        $this->collections = Cache::flexible('collections', [172800, 259200], function () {
             return Collection::where('promote', true)->orderBy('sort_order')->take(10)->get(['title', 'image'])->toArray();
         });
     }

diff --git a/app/Livewire/MoleculeDetails.php b/app/Livewire/MoleculeDetails.php
@@ -24,7 +24,7 @@ public function rendered()
         $_molecule = Cache::get('molecules.'.$id);
         if ($_molecule && ! $_molecule->relationLoaded('properties')) {
             Cache::forget('molecules.'.$id);
-            Cache::remember('molecules.'.$id, 172800, function () use ($molecule) {
+            Cache::flexible('molecules.'.$id, [172800, 259200], function () use ($molecule) {
                 $molecule['schema'] = $molecule->getSchema();
 
                 return $molecule;

diff --git a/app/Livewire/RecentMolecules.php b/app/Livewire/RecentMolecules.php
@@ -16,7 +16,7 @@ class RecentMolecules extends Component
     public function render()
     {
         return view('livewire.recent-molecules', [
-            'molecules' => Cache::remember('molecules.recent', 172800, function () {
+            'molecules' => Cache::flexible('molecules.recent', [172800, 259200], function () {
                 return Molecule::where('is_parent', false)->where('active', true)->where('name', '!=', null)->where('annotation_level', '=', 5)->orderByDesc('updated_at')->paginate($this->size);
             }),
         ]);

diff --git a/app/Livewire/Welcome.php b/app/Livewire/Welcome.php
@@ -3,6 +3,7 @@
 namespace App\Livewire;
 
 use Illuminate\Support\Facades\Cache;
+use Illuminate\Support\Facades\DB;
 use Livewire\Attributes\Lazy;
 use Livewire\Attributes\Url;
 use Livewire\Component;
@@ -51,10 +52,18 @@ public function placeholder()
 
     public function render()
     {
-        $this->totalMolecules = Cache::get('stats.molecules');
-        $this->totalCollections = Cache::get('stats.collections', 0);
-        $this->uniqueOrganisms = Cache::get('stats.organisms', 0);
-        $this->citationsMapped = Cache::get('stats.citations', 0);
+        $this->totalMolecules = Cache::flexible('stats.molecules', [172800, 259200], function () {
+            return DB::table('molecules')->selectRaw('count(*)')->whereRaw('active=true and NOT (is_parent=true AND has_variants=true)')->get()[0]->count;
+        });
+        $this->totalCollections = Cache::flexible('stats.collections', [172800, 259200], function () {
+            return DB::table('collections')->selectRaw('count(*)')->get()[0]->count;
+        });
+        $this->uniqueOrganisms = Cache::flexible('stats.organisms', [172800, 259200], function () {
+            return DB::table('organisms')->selectRaw('count(*)')->get()[0]->count;
+        });
+        $this->citationsMapped = Cache::flexible('stats.citations', [172800, 259200], function () {
+            return DB::table('citations')->selectRaw('count(*)')->get()[0]->count;
+        });
 
         return view('livewire.welcome', [
             'totalMolecules' => $this->totalMolecules,