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feat: various ux/ui updates and other minor changes
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,65 @@ | ||
| <?php | ||
|
|
||
| namespace App\Console\Commands; | ||
|
|
||
| use App\Models\Molecule; | ||
| use DB; | ||
| use Illuminate\Console\Command; | ||
|
|
||
| class ExtractCAS extends Command | ||
| { | ||
| /** | ||
| * The name and signature of the console command. | ||
| * | ||
| * @var string | ||
| */ | ||
| protected $signature = 'app:extract-cas'; | ||
|
|
||
| /** | ||
| * The console command description. | ||
| * | ||
| * @var string | ||
| */ | ||
| protected $description = 'Command description'; | ||
|
|
||
| /** | ||
| * Execute the console command. | ||
| */ | ||
| public function handle() | ||
| { | ||
| Molecule::whereNull('cas')->whereNotNull('synonyms')->select('id', 'synonyms')->chunk(10000, function ($mols) { | ||
| $data = []; | ||
| $pattern = "/\b[1-9][0-9]{1,5}-\d{2}-\d\b/"; | ||
| foreach ($mols as $mol) { | ||
| $casIds = preg_grep($pattern, $mol->synonyms); | ||
| array_push($data, [ | ||
| 'id' => $mol->id, | ||
| 'cas' => array_values($casIds), | ||
| ]); | ||
| $this->info("Mapped and updated: $mol->id"); | ||
| } | ||
| $this->insertBatch($data); | ||
| }); | ||
| } | ||
|
|
||
| /** | ||
| * Insert a batch of data into the database. | ||
| * | ||
| * @return void | ||
| */ | ||
| private function insertBatch(array $data) | ||
| { | ||
| DB::transaction(function () use ($data) { | ||
| foreach ($data as $row) { | ||
| Molecule::updateorCreate( | ||
| [ | ||
| 'id' => $row['id'], | ||
| ], | ||
| [ | ||
| 'cas' => $row['cas'], | ||
| ] | ||
| ); | ||
| } | ||
| }); | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,107 @@ | ||
| <?php | ||
|
|
||
| namespace App\Console\Commands; | ||
|
|
||
| use App\Models\Molecule; | ||
| use DB; | ||
| use Illuminate\Console\Command; | ||
|
|
||
| class GenerateAnnotationScore extends Command | ||
| { | ||
| /** | ||
| * The name and signature of the console command. | ||
| * | ||
| * @var string | ||
| */ | ||
| protected $signature = 'app:generate-score'; | ||
|
|
||
| /** | ||
| * The console command description. | ||
| * | ||
| * @var string | ||
| */ | ||
| protected $description = 'Command description'; | ||
|
|
||
| public function handle() | ||
| { | ||
| $batchSize = 1000; | ||
| $offset = 0; | ||
|
|
||
| while (true) { | ||
| $molecules = DB::table('molecules') | ||
| ->offset($offset) | ||
| ->limit($batchSize) | ||
| ->get(); | ||
|
|
||
| if ($molecules->isEmpty()) { | ||
| break; | ||
| } | ||
|
|
||
| $data = []; | ||
|
|
||
| foreach ($molecules as $molecule) { | ||
| $score = $this->calculateAnnotationScore($molecule); | ||
| array_push($data, [ | ||
| 'id' => $molecule->id, | ||
| 'annotation_level' => $score, | ||
| ]); | ||
| } | ||
|
|
||
| $this->insertBatch($data); | ||
|
|
||
| $offset += $batchSize; | ||
| $this->info("Processed batch starting from offset $offset"); | ||
| } | ||
|
|
||
| $this->info('Annotation scores generated successfully.'); | ||
| } | ||
|
|
||
| /** | ||
| * Insert a batch of data into the database. | ||
| * | ||
| * @return void | ||
| */ | ||
| private function insertBatch(array $data) | ||
| { | ||
| DB::transaction(function () use ($data) { | ||
| foreach ($data as $row) { | ||
| Molecule::updateorCreate( | ||
| [ | ||
| 'id' => $row['id'], | ||
| ], | ||
| [ | ||
| 'annotation_level' => $row['annotation_level'], | ||
| ] | ||
| ); | ||
| } | ||
| }); | ||
| } | ||
|
|
||
| protected function calculateAnnotationScore($molecule) | ||
| { | ||
| $literatureCount = DB::table('citables') | ||
| ->where('citable_id', $molecule->id) | ||
| ->where('citable_type', 'App\Models\Molecule') | ||
| ->count(); | ||
|
|
||
| $organismCount = DB::table('molecule_organism') | ||
| ->where('molecule_id', $molecule->id) | ||
| ->count(); | ||
|
|
||
| $casScore = $molecule->cas ? 1 : 0.5; | ||
| $synonymsScore = $molecule->synonyms ? (count(explode(',', $molecule->synonyms)) >= 3 ? 1 : 0.5) : 0; | ||
| $nameScore = $molecule->name ? 1 : 0.5; | ||
|
|
||
| $literatureScore = $literatureCount >= 3 ? 1 : ($literatureCount >= 1 ? 0.5 : 0); | ||
| $organismScore = $organismCount >= 1 ? 1 : 0; | ||
|
|
||
| $totalScore = ($literatureScore * 0.30) + | ||
| ($organismScore * 0.25) + | ||
| ($casScore * 0.20) + | ||
| ($synonymsScore * 0.15) + | ||
| ($nameScore * 0.10); | ||
| $finalScore = round($totalScore * 5, 2); | ||
|
|
||
| return ceil($finalScore); | ||
| } | ||
| } |
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