feat: Add job for metadata extraction and generate BagIt packages

.env.example

@@ -24,6 +24,17 @@ COOL_OFF_PERIOD=10
 SCHEMA_VERSION=beta
 BACKUP_KEEP_DAYS=7
 
+# Spectra Parsing Configuration
+NMRKIT_API_URL=https://nmrkit.nmrxiv.org/latest/spectra/parse/url
+BIOSCHEMA_API_URL=https://nmrxiv.org/api/v1/schemas/bioschemas
+SPECTRA_STORAGE_DISK=local
+SPECTRA_STORAGE_PATH=spectra_parse
+SPECTRA_JOB_TRIES=3
+SPECTRA_JOB_TIMEOUT=600
+SPECTRA_RETRY_COUNT=3
+SPECTRA_DOWNLOAD_TIMEOUT=300
+SPECTRA_API_TIMEOUT=300
+
 # ============================================================================
 # Logging Configuration
 # ============================================================================

.gitignore

@@ -6,6 +6,7 @@
 /public/vendor/swagger-api
 /storage/*.key
 /storage/pail
+/storage/app/spectra_parse
 /vendor
 .env
 .env.production

app/Console/Commands/QueueMetadataExtractionBagitGenerationJobs.php

@@ -0,0 +1,126 @@
+<?php
+
+namespace App\Console\Commands;
+
+use App\Jobs\ProcessMetadataExtractionBagitGenerationJob;
+use App\Models\Study;
+use Illuminate\Console\Command;
+
+class QueueMetadataExtractionBagitGenerationJobs extends Command
+{
+    /**
+     * The name and signature of the console command.
+     *
+     * @var string
+     */
+    protected $signature = 'nmrxiv:queue-metadata-extraction
+                            {--limit= : Limit number of studies to process}
+                            {--ids= : Comma-separated study IDs to process}
+                            {--fresh : Clear existing status and start fresh}
+                            {--retry-failed : Retry failed jobs}';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'Queue metadata extraction and BagIt generation jobs for eligible studies';
+
+    /**
+     * Execute the console command.
+     */
+    public function handle(): int
+    {
+        if ($this->option('fresh')) {
+            if ($this->confirm('This will reset all BagIt status for all studies. Continue?', false)) {
+                Study::query()->update([
+                    'metadata_bagit_generation_status' => null,
+                    'metadata_bagit_generation_logs' => null,
+                ]);
+                $this->info('✓ Cleared all existing BagIt status data');
+            } else {
+                return self::SUCCESS;
+            }
+        }
+
+        $query = Study::query()
+            ->where('has_nmrium', true)
+            ->where('is_public', true)
+            ->whereNotNull('download_url');
+
+        // Filter by specific study IDs if provided
+        if ($ids = $this->option('ids')) {
+            $studyIds = array_map('trim', explode(',', $ids));
+            $query->whereIn('id', $studyIds);
+            $this->info('Processing '.count($studyIds).' specific study IDs...');
+        }
+
+        if ($this->option('retry-failed')) {
+            // Get failed study IDs from database
+            $failedStudies = Study::where('metadata_bagit_generation_status', 'failed')->get();
+
+            if ($failedStudies->isEmpty()) {
+                $this->warn('No failed jobs to retry.');
+
+                return self::SUCCESS;
+            }
+
+            $query->whereIn('id', $failedStudies->pluck('id'));
+            $this->info('Retrying '.$failedStudies->count().' failed jobs...');
+
+            // Reset status to pending
+            Study::where('metadata_bagit_generation_status', 'failed')
+                ->whereIn('id', $failedStudies->pluck('id'))
+                ->update(['metadata_bagit_generation_status' => 'pending']);
+        } elseif (! $this->option('ids')) {
+            // Only exclude already processed studies when not targeting specific IDs
+            $query->where(function ($q) {
+                $q->whereNull('metadata_bagit_generation_status')
+                    ->orWhereIn('metadata_bagit_generation_status', ['failed']);
+            });
+        }
+
+        if ($limit = $this->option('limit')) {
+            $query->limit((int) $limit);
+        }
+
+        $studies = $query->get();
+
+        if ($studies->isEmpty()) {
+            $this->warn('No eligible studies found to process.');
+
+            return self::SUCCESS;
+        }
+
+        $this->info("Found {$studies->count()} studies to process");
+
+        $bar = $this->output->createProgressBar($studies->count());
+        $bar->setFormat('verbose');
+
+        $jobsDispatched = 0;
+
+        foreach ($studies as $study) {
+            // Mark as pending with queued timestamp
+            $study->update([
+                'metadata_bagit_generation_status' => 'pending',
+                'metadata_bagit_generation_logs' => [
+                    'queued_at' => now()->toIso8601String(),
+                    'study_identifier' => str_replace('NMRXIV:', '', $study->identifier),
+                ],
+            ]);
+
+            // Dispatch job to queue
+            ProcessMetadataExtractionBagitGenerationJob::dispatch($study->id);
+
+            $jobsDispatched++;
+            $bar->advance();
+        }
+
+        $bar->finish();
+        $this->newLine(2);
+
+        $this->info("✓ Successfully dispatched {$jobsDispatched} jobs to the queue");
+
+        return self::SUCCESS;
+    }
+}