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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,94 @@ | ||
| <?php | ||
|
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| namespace App\Console\Commands; | ||
|
|
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| use Illuminate\Console\Command; | ||
| use Illuminate\Support\Facades\DB; | ||
| use Illuminate\Support\Facades\Storage; | ||
|
|
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| class ExportMoleculesWithOrganisms extends Command | ||
| { | ||
| /** | ||
| * The name and signature of the console command. | ||
| * | ||
| * @var string | ||
| */ | ||
| protected $signature = 'app:export-molecules-with-organisms'; | ||
|
|
||
| /** | ||
| * The console command description. | ||
| * | ||
| * @var string | ||
| */ | ||
| protected $description = 'Command description'; | ||
|
|
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| /** | ||
| * Execute the console command. | ||
| */ | ||
| /** | ||
| * Execute the console command. | ||
| * | ||
| * @return mixed | ||
| */ | ||
| public function handle() | ||
| { | ||
| // Fetch the data | ||
| $data = DB::table('molecule_organism') | ||
| ->join('molecules', 'molecule_organism.molecule_id', '=', 'molecules.id') | ||
| ->join('organisms', 'molecule_organism.organism_id', '=', 'organisms.id') | ||
| ->select('molecule_organism.molecule_id', 'molecules.cas', 'molecules.canonical_smiles', 'molecules.identifier', | ||
| 'organisms.name as organism_name', 'organisms.iri as organism_iri', 'organisms.rank as organism_rank', | ||
| 'molecule_organism.*') | ||
| ->get(); | ||
|
|
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| // Group by molecule_id and concatenate values | ||
| $groupedData = $data->groupBy('molecule_id')->map(function ($rows) { | ||
| $firstRow = $rows->first(); | ||
| $moleculeId = $firstRow->molecule_id; | ||
| $moleculeCasArray = json_decode($firstRow->cas, true); | ||
| $moleculeCas = is_array($moleculeCasArray) && ! empty($moleculeCasArray) ? $moleculeCasArray[0] : null; | ||
| $canonicalSmiles = $firstRow->canonical_smiles; | ||
| $identifier = $firstRow->identifier; | ||
|
|
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| $organisms = $rows->map(function ($row) { | ||
| $organismDetail = $row->organism_name; | ||
| if (! empty($row->organism_iri)) { | ||
| $organismDetail .= ' ('.urldecode($row->organism_iri).'|'.$row->organism_rank.')'; | ||
| } | ||
|
|
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| return $organismDetail; | ||
| })->implode('|'); | ||
|
|
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| // Get pivot columns, assuming the pivot table has additional columns like 'attribute1' and 'attribute2' | ||
| $pivotColumns = ['attribute1', 'attribute2']; | ||
| $pivotData = []; | ||
| foreach ($pivotColumns as $column) { | ||
| $pivotData[$column] = $rows->pluck($column)->unique()->implode('|'); | ||
| } | ||
|
|
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| return array_merge([ | ||
| 'molecule_id' => $moleculeId, | ||
| 'identifier' => $identifier, | ||
| 'molecule_cas' => $moleculeCas, | ||
| 'canonical_smiles' => $canonicalSmiles, | ||
| 'organisms' => $organisms, | ||
| ], $pivotData); | ||
| }); | ||
|
|
||
| // Convert to CSV format | ||
| $csvContent = $groupedData->map(function ($row) { | ||
| return implode(',', array_map(function ($value) { | ||
| return '"'.str_replace('"', '""', $value).'"'; | ||
| }, $row)); | ||
| })->prepend(implode(',', array_keys($groupedData->first())))->implode("\n"); | ||
|
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| // Save to a CSV file | ||
| // The file will be created in the storage/app directory | ||
| Storage::put('molecules_with_organisms.csv', $csvContent); | ||
|
|
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| // Alternatively, to save in the storage/app/public directory: | ||
| // Storage::put('public/molecules_with_organisms.csv', $csvContent); | ||
|
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| $this->info('Export completed successfully.'); | ||
| } | ||
| } |
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