feat: new command to import np classifier columns

app/Console/Commands/ImportNPClassifierOutput.php

@@ -0,0 +1,95 @@
+<?php
+
+namespace App\Console\Commands;
+
+use App\Models\Molecule;
+use DB;
+use Illuminate\Console\Command;
+use Log;
+
+class ImportNPClassifierOutput extends Command
+{
+    /**
+     * The name and signature of the console command.
+     *
+     * @var string
+     */
+    protected $signature = 'coconut:import-np-classifier-output  {file}';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'Command description';
+
+    /**
+     * Execute the console command.
+     */
+    public function handle()
+    {
+        $file = storage_path($this->argument('file'));
+
+        if (! file_exists($file) || ! is_readable($file)) {
+            $this->error('File not found or not readable.');
+
+            return 1;
+        }
+
+        Log::info('Reading file: '.$file);
+
+        $batchSize = 10000;
+        $header = null;
+        $data = [];
+        $rowCount = 0;
+
+        if (($handle = fopen($file, 'r')) !== false) {
+            while (($row = fgetcsv($handle, 0, "\t")) !== false) {
+                if (! $header) {
+                    $header = $row;
+                } else {
+                    try {
+                        $data[] = array_combine($header, $row);
+                        $rowCount++;
+                        if ($rowCount % $batchSize == 0) {
+                            $this->insertBatch($data);
+                            $this->info('Rows inserted: '.$rowCount);
+                            $data = [];
+                        }
+                    } catch (\ValueError $e) {
+                        Log::info('An error occurred: '.$e->getMessage());
+                        Log::info($rowCount++);
+                    }
+                }
+            }
+            fclose($handle);
+
+            if (! empty($data)) {
+                $this->insertBatch($data);
+            }
+        }
+
+        $this->info('Data imported successfully!');
+
+        return 0;
+    }
+
+    /**
+     * Insert a batch of data into the database.
+     *
+     * @return void
+     */
+    private function insertBatch(array $data)
+    {
+        DB::transaction(function () use ($data) {
+            foreach ($data as $row) {
+                $properties = Molecule::where('identifier', $row['identifier'])->first()->properties()->get()[0];
+                $properties['pathway_results'] = $row['pathway_results'] == '' ? null : $row['pathway_results'];
+                $properties['superclass_results'] = $row['superclass_results'] == '' ? null : $row['superclass_results'];
+                $properties['class_results'] = $row['class_results'] == '' ? null : $row['class_results'];
+                $properties['isglycoside'] = $row['isglycoside'] == '' ? null : $row['isglycoside'];
+                $properties->save();
+            }
+        });
+    }
+}

app/Helper.php

@@ -168,6 +168,13 @@ function customAuditLog($event_type, $model_objects, $column_name, $currentValue
 
 function changeAudit(array $data): array
 {
+    // set the user_id and user_type if they are null (commands)
+    if (! $data['user_id']) {
+        $data['user_id'] = 11;
+    }
+    if (! $data['user_type']) {
+        $data['user_type'] = 'App\Models\User';
+    }
 
     if (($data['event'] === 're-assign' || $data['event'] === 'detach' || $data['event'] === 'attach' || $data['event'] === 'sync') && $data['old_values'] && $data['new_values']) {
         $whitelist = [

app/Livewire/MoleculeHistoryTimeline.php

@@ -22,8 +22,8 @@ public function getHistory()
             //     $audit_data[$index]['affected_columns'][$key]['new_value'] = $value['new']??null;
             // }
 
-            $old_key = explode('.', array_keys($audit->old_values)[0]??null)[0]??'none';
-            $new_key = explode('.', array_keys($audit->new_values)[0]??null)[0]??'none';
+            $old_key = $audit->old_values ? explode('.', array_keys($audit->old_values)[0])[0] : null;
+            $new_key = $audit->new_values ? explode('.', array_keys($audit->new_values)[0])[0] : null;
 
             $old_key = $old_key ?: $new_key;
             $new_key = $new_key ?: $old_key;

app/Models/Properties.php

@@ -60,6 +60,9 @@ class Properties extends Model implements Auditable
         'chemical_sub_class' => 'array',
         'chemical_super_class' => 'array',
         'direct_parent_classification' => 'array',
+        'pathway_results' => 'array',
+        'superclass_results' => 'array',
+        'class_results' => 'array',
     ];
 
     /**
@@ -71,4 +74,9 @@ public function molecule()
     {
         return $this->belongsTo(Molecule::class, 'molecule_id');
     }
+
+    public function transformAudit(array $data): array
+    {
+        return changeAudit($data);
+    }
 }

database/migrations/2024_09_09_150750_change_columns_on_molecules_table.php

@@ -22,7 +22,7 @@ public function up(): void
     public function down(): void
     {
         Schema::table('molecules', function (Blueprint $table) {
-            $table->json('comment')->nullable()->change();
+            // $table->json('comment')->nullable()->change();
         });
     }
 };

database/migrations/2024_09_18_150749_add_columns_on_properties_table.php

@@ -0,0 +1,32 @@
+<?php
+
+use Illuminate\Database\Migrations\Migration;
+use Illuminate\Database\Schema\Blueprint;
+use Illuminate\Support\Facades\Schema;
+
+return new class extends Migration
+{
+    /**
+     * Run the migrations.
+     */
+    public function up(): void
+    {
+        Schema::table('properties', function (Blueprint $table) {
+            $table->text('pathway_results')->nullable();
+            $table->text('superclass_results')->nullable();
+            $table->text('class_results')->nullable();
+            $table->boolean('isglycoside')->nullable();
+
+        });
+    }
+
+    /**
+     * Reverse the migrations.
+     */
+    public function down(): void
+    {
+        Schema::table('properties', function (Blueprint $table) {
+            $table->dropColumn(['pathway_results', 'superclass_results', 'class_results', 'isglycoside']);
+        });
+    }
+};