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fix(commands): migrate NPEdia links to new RIKEN domain #821

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fix(commands): migrate NPEdia links to new RIKEN domain #821

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267 changes: 267 additions & 0 deletions app/Console/Commands/UpdateNpediaLinks.php
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<?php

namespace App\Console\Commands;

use App\Models\Collection;
use App\Models\Entry;
use App\Models\Molecule;
use Illuminate\Console\Command;
use Illuminate\Support\Facades\DB;
use Illuminate\Support\Facades\Event;
use Illuminate\Support\Facades\Log;
use OwenIt\Auditing\Events\AuditCustom;

class UpdateNpediaLinks extends Command
{
private const COLLECTION_TITLE = 'NPEdia';

private const OLD_ENTRY_LINK_PREFIX = 'http://www.cbrg.riken.jp/npedia/results.php?ID=';

private const NEW_ENTRY_LINK_PREFIX = 'https://npedia.riken.jp/npedia/details.php?ID=';

private const OLD_COLLECTION_URL = 'http://www.cbrg.riken.jp/npedia/';

private const NEW_COLLECTION_URL = 'https://npedia.riken.jp/npedia/';

/**
* The name and signature of the console command.
*
* @var string
*/
protected $signature = 'coconut:update-npedia-links
{--dry-run : Preview counts and sample changes without writing}
{--batch=500 : Number of records to process per batch}';

/**
* The console command description.
*
* @var string
*/
protected $description = 'Update NPEdia source links to the new RIKEN domain (issue #690) with audit trail';

public function handle(): int
{
$collection = Collection::where('title', self::COLLECTION_TITLE)->first();

if (! $collection) {
$this->error('NPEdia collection not found.');

return self::FAILURE;
}

$batchSize = max(1, (int) $this->option('batch'));
$dryRun = (bool) $this->option('dry-run');

$entryCount = Entry::query()
->where('collection_id', $collection->id)
->where('link', 'like', self::OLD_ENTRY_LINK_PREFIX.'%')
->count();

$pivotCount = DB::table('collection_molecule')
->where('collection_id', $collection->id)
->where('url', 'like', '%'.self::OLD_ENTRY_LINK_PREFIX.'%')
->count();

$collectionNeedsUpdate = $collection->url === self::OLD_COLLECTION_URL;

$this->info("NPEdia collection ID: {$collection->id}");
$this->info('Entries to update: '.$entryCount);
$this->info('Collection-molecule pivots to update: '.$pivotCount);
$this->info('Collection URL to update: '.($collectionNeedsUpdate ? 'yes' : 'no'));

if ($dryRun) {
$this->warn('Dry run enabled — no changes were written.');

$sampleEntry = Entry::query()
->where('collection_id', $collection->id)
->where('link', 'like', self::OLD_ENTRY_LINK_PREFIX.'%')
->first(['reference_id', 'link']);

if ($sampleEntry) {
$this->line('Sample entry link:');
$this->line(' old: '.$sampleEntry->link);
$this->line(' new: '.$this->replaceEntryLink($sampleEntry->link));
}

$samplePivot = DB::table('collection_molecule')
->where('collection_id', $collection->id)
->where('url', 'like', '%'.self::OLD_ENTRY_LINK_PREFIX.'%')
->value('url');

if ($samplePivot) {
$this->line('Sample pivot url:');
$this->line(' old: '.$samplePivot);
$this->line(' new: '.$this->replaceEntryLink($samplePivot));
}

if ($collectionNeedsUpdate) {
$this->line('Collection url:');
$this->line(' old: '.self::OLD_COLLECTION_URL);
$this->line(' new: '.self::NEW_COLLECTION_URL);
}

return self::SUCCESS;
}

try {
$this->updateCollectionUrl($collection, $collectionNeedsUpdate);
$entriesUpdated = $this->updateEntries($collection->id, $batchSize, $entryCount);
$pivotsUpdated = $this->updateCollectionMoleculePivots($collection->id, $batchSize, $pivotCount);

$this->info('Updated collection URL: '.($collectionNeedsUpdate ? 'yes' : 'skipped (already current)'));
$this->info("Updated {$entriesUpdated} entries.");
$this->info("Updated {$pivotsUpdated} collection-molecule pivots.");

return self::SUCCESS;
} catch (\Throwable $e) {
Log::error('NPEdia link update failed: '.$e->getMessage(), [
'exception' => $e,
]);
$this->error('Update failed: '.$e->getMessage());

return self::FAILURE;
}
}

private function updateCollectionUrl(Collection $collection, bool $needsUpdate): void
{
if (! $needsUpdate) {
return;
}

$collection->url = self::NEW_COLLECTION_URL;
$collection->save();
}

private function updateEntries(int $collectionId, int $batchSize, int $total): int
{
$updated = 0;
$progressBar = $this->output->createProgressBar($total);
$progressBar->start();

Entry::query()
->where('collection_id', $collectionId)
->where('link', 'like', self::OLD_ENTRY_LINK_PREFIX.'%')
->orderBy('id')
->chunkById($batchSize, function ($entries) use (&$updated, $progressBar) {
DB::transaction(function () use ($entries, &$updated, $progressBar) {
foreach ($entries as $entry) {
$newLink = $this->replaceEntryLink($entry->link);

if ($newLink === $entry->link) {
$progressBar->advance();

continue;
}

$entry->link = $newLink;
$entry->meta_data = $this->replaceMetaDataUrl($entry->meta_data);
$entry->save();
$updated++;
$progressBar->advance();
}
});
});

$progressBar->finish();
$this->newLine();

return $updated;
}

private function updateCollectionMoleculePivots(int $collectionId, int $batchSize, int $total): int
{
$updated = 0;
$progressBar = $this->output->createProgressBar($total);
$progressBar->start();

DB::table('collection_molecule')
->where('collection_id', $collectionId)
->where('url', 'like', '%'.self::OLD_ENTRY_LINK_PREFIX.'%')
->orderBy('molecule_id')
->chunk($batchSize, function ($pivots) use ($collectionId, &$updated, $progressBar) {
DB::transaction(function () use ($pivots, $collectionId, &$updated, $progressBar) {
$bulkUpdates = [];
$auditEvents = [];

$moleculeIds = $pivots->pluck('molecule_id')->all();
$molecules = Molecule::query()->findMany($moleculeIds)->keyBy('id');

foreach ($pivots as $pivot) {
$newUrl = $this->replaceEntryLink($pivot->url);

if ($newUrl === $pivot->url) {
continue;
}

$bulkUpdates[] = [
'molecule_id' => $pivot->molecule_id,
'collection_id' => $collectionId,
'url' => $newUrl,
'reference' => $pivot->reference,
];

$molecule = $molecules->get($pivot->molecule_id);
if ($molecule) {
$auditEvents[] = [
'molecule' => $molecule,
'old' => ['url' => $pivot->url],
'new' => ['url' => $newUrl],
];
}

$updated++;
$progressBar->advance();
}

foreach (array_chunk($bulkUpdates, 100) as $chunk) {
DB::table('collection_molecule')->upsert(
$chunk,
['molecule_id', 'collection_id'],
['url']
);
}

foreach (array_chunk($auditEvents, 50) as $chunk) {
foreach ($chunk as $audit) {
$molecule = $audit['molecule'];
$molecule->auditEvent = 'npediaLinkUpdate';
$molecule->isCustomEvent = true;
$molecule->auditCustomOld = $audit['old'];
$molecule->auditCustomNew = $audit['new'];
Event::dispatch(AuditCustom::class, [$molecule]);
}
}
});
});

$progressBar->finish();
$this->newLine();

return $updated;
}

private function replaceEntryLink(?string $value): ?string
{
if ($value === null || $value === '') {
return $value;
}

return str_replace(self::OLD_ENTRY_LINK_PREFIX, self::NEW_ENTRY_LINK_PREFIX, $value);
}

/**
* @param array<string, mixed>|null $metaData
* @return array<string, mixed>|null
*/
private function replaceMetaDataUrl(?array $metaData): ?array
{
if (! is_array($metaData) || ! isset($metaData['m']['url'])) {
return $metaData;
}

$metaData['m']['url'] = $this->replaceEntryLink($metaData['m']['url']);

return $metaData;
}
}
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