Organism resource improvements

app/Console/Commands/MapOrganismNamesToOGG.php

@@ -54,7 +54,7 @@ public function handle()
                         } else {
                             $data = $this->getOLSIRI(explode(' ', $name)[0], 'family');
                             if ($data) {
-                                $this->updateOrganismModel($name, $data, $organism, 'genus');
+                                $this->updateOrganismModel($name, $data, $organism, 'family');
                                 $this->info("Mapped and updated: $name");
                             } else {
                                 $this->getGNFMatches($name, $organism);
@@ -155,7 +155,7 @@ protected function getOLSIRI($name, $rank)
             if (isset($data['elements']) && count($data['elements']) > 0) {
 
                 $element = $data['elements'][0];
-                if (isset($element['iri'], $element['ontologyId']) && $element['isObsolete'] === 'false') {
+                if (isset($element['iri'], $element['ontologyId']) && $element['isObsolete'] === false) {
                     if ($rank && $rank == 'species') {
                         if (isset($element['http://purl.obolibrary.org/obo/ncbitaxon#has_rank']) && $element['http://purl.obolibrary.org/obo/ncbitaxon#has_rank'] == 'http://purl.obolibrary.org/obo/NCBITaxon_species') {
                             return urlencode($element['iri']);
@@ -188,6 +188,10 @@ protected function updateOrganismModel($name, $iri, $organism = null, $rank = nu
         if ($organism) {
             $organism->iri = $iri;
             $organism->rank = $rank;
+            // Auto-generate slug if not exists
+            if (! $organism->slug) {
+                $organism->slug = \Illuminate\Support\Str::slug($name);
+            }
             $organism->save();
         } else {
             $this->error("Organism not found in the database: $name");

app/Filament/Dashboard/Resources/CitationResource.php

@@ -2,13 +2,17 @@
 
 namespace App\Filament\Dashboard\Resources;
 
-use App\Filament\Dashboard\Resources\CitationResource\Pages;
+use App\Filament\Dashboard\Resources\CitationResource\Pages\CreateCitation;
+use App\Filament\Dashboard\Resources\CitationResource\Pages\EditCitation;
+use App\Filament\Dashboard\Resources\CitationResource\Pages\ListCitations;
 use App\Filament\Dashboard\Resources\CitationResource\RelationManagers\CollectionRelationManager;
 use App\Filament\Dashboard\Resources\CitationResource\RelationManagers\MoleculeRelationManager;
 use App\Models\Citation;
-use Filament\Forms\Form;
+use Filament\Actions\BulkActionGroup;
+use Filament\Actions\DeleteBulkAction;
+use Filament\Actions\EditAction;
 use Filament\Resources\Resource;
-use Filament\Tables;
+use Filament\Schemas\Schema;
 use Filament\Tables\Columns\TextColumn;
 use Filament\Tables\Table;
 use Illuminate\Support\Facades\Cache;
@@ -17,20 +21,20 @@
 
 class CitationResource extends Resource
 {
-    protected static ?string $navigationGroup = 'Data';
+    protected static string|\UnitEnum|null $navigationGroup = 'Data';
 
     protected static ?string $model = Citation::class;
 
     protected static ?string $recordTitleAttribute = 'title';
 
     protected static ?int $navigationSort = 2;
 
-    protected static ?string $navigationIcon = 'heroicon-o-ticket';
+    protected static string|\BackedEnum|null $navigationIcon = 'heroicon-o-ticket';
 
-    public static function form(Form $form): Form
+    public static function form(Schema $schema): Schema
     {
-        return $form
-            ->schema(Citation::getForm());
+        return $schema
+            ->components(Citation::getForm());
     }
 
     public static function table(Table $table): Table
@@ -47,12 +51,13 @@ public static function table(Table $table): Table
             ->filters([
                 //
             ])
-            ->actions([
-                Tables\Actions\EditAction::make(),
+            ->recordActions([
+                EditAction::make()
+                    ->iconButton(),
             ])
-            ->bulkActions([
-                Tables\Actions\BulkActionGroup::make([
-                    Tables\Actions\DeleteBulkAction::make(),
+            ->toolbarActions([
+                BulkActionGroup::make([
+                    DeleteBulkAction::make(),
                 ]),
             ]);
     }
@@ -69,9 +74,9 @@ public static function getRelations(): array
     public static function getPages(): array
     {
         return [
-            'index' => Pages\ListCitations::route('/'),
-            'create' => Pages\CreateCitation::route('/create'),
-            'edit' => Pages\EditCitation::route('/{record}/edit'),
+            'index' => ListCitations::route('/'),
+            'create' => CreateCitation::route('/create'),
+            'edit' => EditCitation::route('/{record}/edit'),
         ];
     }
 

app/Filament/Dashboard/Resources/CitationResource/Pages/EditCitation.php

@@ -3,7 +3,7 @@
 namespace App\Filament\Dashboard\Resources\CitationResource\Pages;
 
 use App\Filament\Dashboard\Resources\CitationResource;
-use Filament\Actions;
+use Filament\Actions\DeleteAction;
 use Filament\Resources\Pages\EditRecord;
 
 class EditCitation extends EditRecord
@@ -13,7 +13,7 @@ class EditCitation extends EditRecord
     protected function getHeaderActions(): array
     {
         return [
-            Actions\DeleteAction::make(),
+            DeleteAction::make(),
         ];
     }
 }

app/Filament/Dashboard/Resources/CitationResource/Pages/ListCitations.php

@@ -3,7 +3,7 @@
 namespace App\Filament\Dashboard\Resources\CitationResource\Pages;
 
 use App\Filament\Dashboard\Resources\CitationResource;
-use Filament\Actions;
+use Filament\Actions\CreateAction;
 use Filament\Resources\Pages\ListRecords;
 
 class ListCitations extends ListRecords
@@ -13,7 +13,7 @@ class ListCitations extends ListRecords
     protected function getHeaderActions(): array
     {
         return [
-            Actions\CreateAction::make(),
+            CreateAction::make(),
         ];
     }
 }

app/Filament/Dashboard/Resources/CitationResource/RelationManagers/CollectionRelationManager.php

@@ -2,19 +2,23 @@
 
 namespace App\Filament\Dashboard\Resources\CitationResource\RelationManagers;
 
-use Filament\Forms\Form;
+use Filament\Actions\BulkActionGroup;
+use Filament\Actions\DeleteAction;
+use Filament\Actions\DeleteBulkAction;
+use Filament\Actions\EditAction;
 use Filament\Resources\RelationManagers\RelationManager;
-use Filament\Tables;
+use Filament\Schemas\Schema;
+use Filament\Tables\Columns\TextColumn;
 use Filament\Tables\Table;
 
 class CollectionRelationManager extends RelationManager
 {
     protected static string $relationship = 'collections';
 
-    public function form(Form $form): Form
+    public function form(Schema $schema): Schema
     {
-        return $form
-            ->schema([
+        return $schema
+            ->components([
             ]);
     }
 
@@ -23,20 +27,20 @@ public function table(Table $table): Table
         return $table
             ->recordTitleAttribute('title')
             ->columns([
-                Tables\Columns\TextColumn::make('title')->wrap(),
+                TextColumn::make('title')->wrap(),
             ])
             ->filters([
                 //
             ])
             ->headerActions([
             ])
-            ->actions([
-                Tables\Actions\EditAction::make(),
-                Tables\Actions\DeleteAction::make(),
+            ->recordActions([
+                EditAction::make(),
+                DeleteAction::make(),
             ])
-            ->bulkActions([
-                Tables\Actions\BulkActionGroup::make([
-                    Tables\Actions\DeleteBulkAction::make(),
+            ->toolbarActions([
+                BulkActionGroup::make([
+                    DeleteBulkAction::make(),
                 ]),
             ]);
     }

app/Filament/Dashboard/Resources/CitationResource/RelationManagers/MoleculeRelationManager.php

@@ -2,19 +2,23 @@
 
 namespace App\Filament\Dashboard\Resources\CitationResource\RelationManagers;
 
-use Filament\Forms\Form;
+use Filament\Actions\BulkActionGroup;
+use Filament\Actions\DeleteAction;
+use Filament\Actions\DeleteBulkAction;
+use Filament\Actions\EditAction;
 use Filament\Resources\RelationManagers\RelationManager;
-use Filament\Tables;
+use Filament\Schemas\Schema;
+use Filament\Tables\Columns\TextColumn;
 use Filament\Tables\Table;
 
 class MoleculeRelationManager extends RelationManager
 {
     protected static string $relationship = 'molecules';
 
-    public function form(Form $form): Form
+    public function form(Schema $schema): Schema
     {
-        return $form
-            ->schema([
+        return $schema
+            ->components([
             ]);
     }
 
@@ -23,20 +27,20 @@ public function table(Table $table): Table
         return $table
             ->recordTitleAttribute('name')
             ->columns([
-                Tables\Columns\TextColumn::make('name'),
+                TextColumn::make('name'),
             ])
             ->filters([
                 //
             ])
             ->headerActions([
             ])
-            ->actions([
-                Tables\Actions\EditAction::make(),
-                Tables\Actions\DeleteAction::make(),
+            ->recordActions([
+                EditAction::make(),
+                DeleteAction::make(),
             ])
-            ->bulkActions([
-                Tables\Actions\BulkActionGroup::make([
-                    Tables\Actions\DeleteBulkAction::make(),
+            ->toolbarActions([
+                BulkActionGroup::make([
+                    DeleteBulkAction::make(),
                 ]),
             ]);
     }