fix: added remove duplicates command

app/Console/Commands/RemoveDuplicates.php

@@ -0,0 +1,210 @@
+<?php
+
+namespace App\Console\Commands;
+
+use App\Models\Molecule;
+use Illuminate\Console\Command;
+use Illuminate\Support\Facades\DB;
+
+class RemoveDuplicates extends Command
+{
+    /**
+     * The name and signature of the console command.
+     *
+     * @var string
+     */
+    protected $signature = 'app:remove-duplicates';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'Command description';
+
+    /**
+     * Execute the console command.
+     */
+    public function handle()
+    {
+        // fetch duplicate parent molecules
+        $fm_results = DB::table('molecules')
+            ->select('canonical_smiles', DB::raw('COUNT(*) as count'))
+            ->where('is_parent', false)
+            ->where('has_stereo', false)
+            ->groupBy('canonical_smiles')
+            ->having(DB::raw('COUNT(*)'), '>', 1)
+            ->get();
+
+        // loop duplicates
+        foreach ($fm_results as $result) {
+            //fetch first entry
+            echo 'Canonical Smiles: '.$result->canonical_smiles.' - Count: '.$result->count."\n";
+            $molecule = Molecule::where('canonical_smiles', $result->canonical_smiles)
+                ->first();
+
+            $remaining_molecules = Molecule::where('canonical_smiles', $result->canonical_smiles)
+                ->where('id', '!=', $molecule->id)
+                ->get();
+
+            $this->merge_data($molecule, $remaining_molecules, 'flat');
+        }
+        echo "\r\n";
+        echo "\r\n";
+
+        // fetch duplicate parent molecules
+        $pm_results = DB::table('molecules')
+            ->select('canonical_smiles', DB::raw('COUNT(*) as count'))
+            ->where('is_parent', true)
+            ->where('has_stereo', false)
+            ->groupBy('canonical_smiles')
+            ->having(DB::raw('COUNT(*)'), '>', 1)
+            ->get();
+
+        echo count($pm_results);
+        echo "\r\n";
+
+        // loop duplicates
+        foreach ($pm_results as $result) {
+            //fetch first entry
+            echo 'Canonical Smiles: '.$result->canonical_smiles.' - Count: '.$result->count."\n";
+            $molecule = Molecule::where('canonical_smiles', $result->canonical_smiles)
+                ->first();
+
+            $remaining_molecules = Molecule::where('canonical_smiles', $result->canonical_smiles)
+                ->where('id', '!=', $molecule->id)
+                ->get();
+
+            $this->merge_data($molecule, $remaining_molecules, 'parent');
+        }
+
+        $sv_results = DB::table('molecules')
+            ->select('canonical_smiles', DB::raw('COUNT(*) as count'))
+            ->where('is_parent', false)
+            ->where('has_stereo', true)
+            ->groupBy('canonical_smiles')
+            ->having(DB::raw('COUNT(*)'), '>', 1)
+            ->get();
+
+        echo count($sv_results);
+        echo "\r\n";
+
+        // loop duplicates
+        foreach ($sv_results as $result) {
+            //fetch first entry
+            echo 'Canonical Smiles: '.$result->canonical_smiles.' - Count: '.$result->count."\n";
+            $molecule = Molecule::where('canonical_smiles', $result->canonical_smiles)
+                ->first();
+
+            $remaining_molecules = Molecule::where('canonical_smiles', $result->canonical_smiles)
+                ->where('id', '!=', $molecule->id)
+                ->get();
+
+            $this->merge_data($molecule, $remaining_molecules, 'parent');
+        }
+    }
+
+    public function merge_data($entry, $duplicates, $type)
+    {
+        DB::transaction(function () use ($entry, $duplicates, $type) {
+            $synonyms = $entry->synonyms ? $entry->synonyms : [];
+            echo $entry->identifier;
+            echo "\r\n";
+            foreach ($duplicates as $duplicate) {
+                // append synonyms
+                $duplicate_synonyms = $duplicate->synonyms ? $duplicate->synonyms : [];
+                $synonyms = array_merge($synonyms, $duplicate_synonyms);
+
+                // update entries table
+                DB::table('entries')
+                    ->select('id')
+                    ->where('molecule_id', $duplicate->id)
+                    ->update(['molecule_id' => $entry->id]);
+
+                // update citables
+                DB::table('citables')
+                    ->where('citable_type', 'App\Models\Molecule')
+                    ->where('citable_id', $duplicate->id)
+                    ->whereNotExists(function ($query) use ($entry) {
+                        $query->select(DB::raw(1))
+                            ->from('citables as c')
+                            ->where('c.citable_type', 'App\Models\Molecule')
+                            ->where('c.citable_id', $entry->id);
+                    })
+                    ->update(['citable_id' => $entry->id]);
+
+                $duplicateEntry = DB::table('collection_molecule')
+                    ->where('molecule_id', $duplicate->id)
+                    ->first();
+
+                if ($duplicateEntry) {
+                    $existingEntry = DB::table('collection_molecule')
+                        ->where('molecule_id', $entry->id)
+                        ->first();
+
+                    if ($existingEntry) {
+                        DB::table('collection_molecule')
+                            ->where('molecule_id', $entry->id)
+                            ->update([
+                                'url' => DB::raw("CONCAT(url, '|', '{$duplicateEntry->url}')"),
+                                'reference' => DB::raw("CONCAT(reference, '|', '{$duplicateEntry->reference}')"),
+                            ]);
+
+                        DB::table('collection_molecule')
+                            ->where('molecule_id', $duplicate->id)
+                            ->delete();
+                    } else {
+                        DB::table('collection_molecule')
+                            ->where('molecule_id', $duplicate->id)
+                            ->update([
+                                'molecule_id' => $entry->id,
+                                'url' => $duplicateEntry->url,
+                                'reference' => $duplicateEntry->reference,
+                            ]);
+                    }
+                }
+
+                // update geo_location_molecule
+                DB::table('geo_location_molecule')
+                    ->where('molecule_id', $duplicate->id)
+                    ->whereNotExists(function ($query) use ($entry) {
+                        $query->select(DB::raw(1))
+                            ->from('geo_location_molecule as glm')
+                            ->where('glm.molecule_id', $entry->id);
+                    })
+                    ->update(['molecule_id' => $entry->id]);
+
+                // update molecule_organism
+                DB::table('molecule_organism')
+                    ->where('molecule_id', $duplicate->id)
+                    ->whereNotExists(function ($query) use ($entry) {
+                        $query->select(DB::raw(1))
+                            ->from('molecule_organism as mo')
+                            ->where('mo.molecule_id', $entry->id);
+                    })
+                    ->update(['molecule_id' => $entry->id]);
+
+                // update molecule_related
+                DB::table('molecule_related')
+                    ->where('molecule_id', $duplicate->id)
+                    ->whereNotExists(function ($query) use ($entry) {
+                        $query->select(DB::raw(1))
+                            ->from('molecule_related as mr')
+                            ->where('mr.molecule_id', $entry->id);
+                    })
+                    ->update(['molecule_id' => $entry->id]);
+
+                if ($type == 'parents') {
+                    $variants = $duplicate->variants();
+                    $variants->update(['parent_id' => $entry->id]);
+                }
+
+                $duplicate->is_duplicate = true;
+                $duplicate->save();
+            }
+
+            $entry->synonyms = $synonyms;
+            $entry->save();
+        });
+    }
+}