feat: new interactive command to reassign molecules to a selected org…

…anism from the list of duplicates based on slug

app/Console/Commands/OrganismDedupeOptions.php

@@ -0,0 +1,125 @@
+<?php
+
+namespace App\Console\Commands;
+
+use Illuminate\Console\Command;
+use Illuminate\Support\Facades\DB;
+use Illuminate\Support\Str;
+use App\Models\Organism;
+
+class OrganismDedupeOptions extends Command
+{
+    /**
+     * The name and signature of the console command.
+     *
+     * @var string
+     */
+    protected $signature = 'app:organism-molecule-counts';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'Find and handle duplicate records in the Organisms (case-insensitive)';
+
+    /**
+     * Execute the console command.
+     */
+    public function handle()
+    {
+        $this->info('Updating missing slugs...');
+
+        DB::statement("UPDATE organisms
+        SET slug = LOWER(
+            REGEXP_REPLACE(
+                REGEXP_REPLACE(name, '^[^A-Za-z]+|[^A-Za-z]+$', '', 'g'),'[^A-Za-z]+|(?<=[a-z])(?=[A-Z])', '-', 'g'))
+        WHERE slug = '' or slug is null;"
+        );
+
+
+        $this->info('Finding duplicate records...');
+        // Query to find duplicates case-insensitively
+        $duplicates = Organism::selectRaw('slug, COUNT(*) as count')
+            ->whereRaw('molecule_count > 0')
+            ->groupBy('slug')
+            ->havingRaw('COUNT(*) > 1')
+            ->pluck('slug')->toArray();
+
+        if (!count($duplicates)) {
+            $this->info('No duplicates found.');
+            return 0;
+        }
+
+
+        // Fetch all records that have duplicates
+        $records = Organism::whereIn('slug', $duplicates)
+            ->get();
+
+        // Group records by the lowercase version of the duplicate column for easier processing
+        $groupedRecords = $records->groupBy('slug');
+
+        foreach ($groupedRecords as $columnValue => $group) {
+            $this->info("Duplicate records found for: {$columnValue}");
+
+            foreach ($group as $index => $record) {
+                $this->info("{$index}: ID = {$record->id}, Column Value = {$record->name}, rank = {$record->rank}, molucule count = {$record->molecule_count}, IRI = {$record->iri}");
+            }
+
+            $retainIndex = $this->ask('Enter the number of the record you want to retain');
+
+            if (is_numeric($retainIndex) && isset($group[$retainIndex])) {
+
+                $selected_organism = $group[$retainIndex];
+                $rest_of_the_organisms = $group->forget($retainIndex);
+
+                foreach ($rest_of_the_organisms as $removable_organism) {
+
+                    DB::transaction(function () use ($selected_organism, $removable_organism) {
+                        DB::beginTransaction();
+                        try {
+                            $moleculeIds = $removable_organism->molecules->pluck('id')->toArray();
+                            // $removable_organism = $this->getOwnerRecord();
+                            $removable_organism->molecules()->detach($moleculeIds);
+
+                            // foreach ($currentOrganism->sampleLocations as $location) {
+                            //     $location->molecules()->detach($moleculeIds);
+                            // }
+                            // $newOrganism = Organism::findOrFail($data['org_id']);
+
+                            // $locations = $livewire->mountedTableBulkActionData['locations'];
+                            // if ($locations) {
+                            //     $sampleLocations = SampleLocation::findOrFail($locations);
+                            //     foreach ($sampleLocations as $location) {
+                            //         $location->molecules()->syncWithoutDetaching($moleculeIds);
+                            //     }
+                            // }
+                            $selected_organism->molecules()->syncWithoutDetaching($moleculeIds);
+
+                            $removable_organism->refresh();
+                            $selected_organism->refresh();
+
+                            $removable_organism->molecule_count = $removable_organism->molecules()->count();
+                            $removable_organism->save();
+                            $selected_organism->molecule_count = $selected_organism->molecules()->count();
+                            $selected_organism->save();
+
+                            DB::commit();
+                        } catch (\Exception $e) {
+                            // Rollback the transaction in case of any error
+                            DB::rollBack();
+                            throw $e; // Optionally rethrow the exception
+                        }
+                    });
+                }
+
+                $this->info("Reassigned molecules to Organism {$selected_organism->name} with ID = {$selected_organism->id}");
+            } else {
+                $this->warn("Invalid selection. No records were deleted for {$columnValue}.");
+            }
+        }
+
+        $this->info('Duplicate handling complete.');
+        return 0;
+    }
+}