fix: delete organisms with no molecules and enables audit trail

Steinbeck-Lab · Aug 26, 2024 · 7ca9c65 · 7ca9c65
1 parent d405d60
commit 7ca9c65
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Showing 4 changed files with 17 additions and 11 deletions.
diff --git a/app/Console/Commands/OrganismDedupeOptions.php b/app/Console/Commands/OrganismDedupeOptions.php
@@ -2,9 +2,10 @@
 
 namespace App\Console\Commands;
 
+use App\Models\Organism;
 use Illuminate\Console\Command;
 use Illuminate\Support\Facades\DB;
-use App\Models\Organism;
+
 use function Laravel\Prompts\select;
 
 class OrganismDedupeOptions extends Command
@@ -37,7 +38,6 @@ public function handle()
         WHERE slug = '' or slug is null;"
         );
 
-
         $this->info('Finding duplicate records...');
 
         // Query to find duplicates case-insensitively
@@ -50,6 +50,7 @@ public function handle()
 
         if (count($duplicates) === 0) {
             $this->info('No duplicates found.');
+
             return 0;
         }
 
@@ -59,6 +60,8 @@ public function handle()
         // Group records by the lowercase version of the duplicate column for easier processing
         $groupedRecords = $records->groupBy('slug');
 
+        $this->info('Found '.count($groupedRecords).' duplicate records.');
+
         foreach ($groupedRecords as $columnValue => $group) {
             $this->info("Duplicate records found for: {$columnValue}");
 
@@ -82,11 +85,14 @@ public function handle()
                         try {
                             $moleculeIds = $removableOrganism->molecules->pluck('id')->toArray();
 
-                            $removableOrganism->molecules()->detach($moleculeIds);
-                            $selectedOrganism->molecules()->syncWithoutDetaching($moleculeIds);
+                            // $removableOrganism->molecules()->detach($moleculeIds);
+                            // $selectedOrganism->molecules()->syncWithoutDetaching($moleculeIds);
+
+                            $removableOrganism->auditDetach('molecules', $moleculeIds);
+                            $selectedOrganism->auditSyncWithoutDetaching('molecules', $moleculeIds);
 
                             $removableOrganism->molecule_count = $removableOrganism->molecules()->count();
-                            $removableOrganism->save();
+                            $removableOrganism->delete();
                             $selectedOrganism->molecule_count = $selectedOrganism->molecules()->count();
                             $selectedOrganism->save();
 
@@ -105,6 +111,7 @@ public function handle()
         }
 
         $this->info('Duplicate handling complete.');
+
         return 0;
     }
 }
diff --git a/app/Console/Commands/OrganismMoleculeCounts.php b/app/Console/Commands/OrganismMoleculeCounts.php
@@ -41,12 +41,11 @@ public function handle()
         }
 
         $this->info('Updatin the residual organisms.');
-        
+
         DB::table('organisms')
             ->whereNotIn('id', $moleculeCounts->pluck('id'))
             ->update(['molecule_count' => 0]);
 
-
         $this->info('Update process completed.');
     }
 }
diff --git a/...lament/Dashboard/Resources/OrganismResource/RelationManagers/MoleculesRelationManager.php b/...lament/Dashboard/Resources/OrganismResource/RelationManagers/MoleculesRelationManager.php
@@ -40,7 +40,7 @@ public function table(Table $table): Table
                 ImageColumn::make('structure')->square()
                     ->label('Structure')
                     ->state(function ($record) {
-                        return env('CM_API', 'https://api.cheminf.studio/latest/') . 'depict/2D?smiles=' . urlencode($record->canonical_smiles) . '&height=300&width=300&CIP=true&toolkit=cdk';
+                        return env('CM_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
                     })
                     ->width(200)
                     ->height(200)
@@ -50,9 +50,9 @@ public function table(Table $table): Table
                 Tables\Columns\TextColumn::make('identifier')->searchable()->toggleable(isToggledHiddenByDefault: true),
                 Tables\Columns\TextColumn::make('name')->searchable()
                     ->formatStateUsing(
-                        fn(Molecule $molecule): HtmlString => new HtmlString("<strong>ID:</strong> {$molecule->id}<br><strong>Identifier:</strong> {$molecule->identifier}<br><strong>Name:</strong> {$molecule->name}")
+                        fn (Molecule $molecule): HtmlString => new HtmlString("<strong>ID:</strong> {$molecule->id}<br><strong>Identifier:</strong> {$molecule->identifier}<br><strong>Name:</strong> {$molecule->name}")
                     )
-                    ->description(fn(Molecule $molecule): string => $molecule->standard_inchi)
+                    ->description(fn (Molecule $molecule): string => $molecule->standard_inchi)
                     ->wrap(),
                 Tables\Columns\TextColumn::make('synonyms')
                     ->searchable()

diff --git a/config/audit.php b/config/audit.php
@@ -181,5 +181,5 @@
     |
     */
 
-    'console' => false,
+    'console' => true,
 ];
-Original file line number
+Diff line change
@@ Expand Up / @@ -181,5 +181,5 @@ @@
         |
         */
-        'console' => false,
+        'console' => true,
     ];