Steinbeck-Lab · sriramkanakam87 · Feb 25, 2026 · Feb 24, 2026 · Feb 24, 2026 · Feb 24, 2026
diff --git a/app/Console/Commands/SubmissionsAutoProcess/ClassifyAuto.php b/app/Console/Commands/SubmissionsAutoProcess/ClassifyAuto.php
@@ -16,7 +16,7 @@ class ClassifyAuto extends Command
     /**
      * The name and signature of the console command.
      */
-    protected $signature = 'coconut:npclassify {collection_id : The ID of the collection to process}';
+    protected $signature = 'coconut:npclassify {collection_id? : The ID of the collection to process} {--all : Process all collections}';
 
     /**
      * The console command description.
@@ -30,40 +30,66 @@ public function handle()
     {
         $collection_id = $this->argument('collection_id');
 
-        $collection = Collection::find($collection_id);
-        if (! $collection) {
-            Log::error("Collection with ID {$collection_id} not found.");
+        if (! $collection_id && ! $this->option('all')) {
+            Log::error('Please specify either a collection_id or use --all flag');
 
             return 1;
         }
 
-        Log::info("Classifying molecules using NPClassifier for collection ID: {$collection_id}");
+        if ($collection_id !== null) {
+            $collection = Collection::find($collection_id);
+            if (! $collection) {
+                Log::error("Collection with ID {$collection_id} not found.");
+
+                return 1;
+            }
+        }
+
+        $collectionLabel = $collection_id !== null ? "collection ID: {$collection_id}" : 'all collections';
+
+        Log::info("Classifying molecules using NPClassifier for {$collectionLabel}");
 
         // Use raw query to avoid ambiguous column issues
-        $sql = '
-            SELECT DISTINCT molecules.id, molecules.canonical_smiles
-            FROM molecules
-            INNER JOIN entries ON entries.molecule_id = molecules.id
-            INNER JOIN properties ON properties.molecule_id = molecules.id
+        $conditions = '
+            WHERE molecules.active = true
+              AND properties.np_classifier_pathway IS NULL
+              AND properties.np_classifier_superclass IS NULL
+              AND properties.np_classifier_class IS NULL
+              AND properties.np_classifier_is_glycoside IS NULL
+        ';
+
+        $bindings = [];
+        if ($collection_id !== null) {
+            $conditions = '
             WHERE entries.collection_id = ?
               AND molecules.active = true
               AND properties.np_classifier_pathway IS NULL
               AND properties.np_classifier_superclass IS NULL
               AND properties.np_classifier_class IS NULL
               AND properties.np_classifier_is_glycoside IS NULL
+            ';
+            $bindings[] = $collection_id;
+        }
+
+        $sql = '
+            SELECT DISTINCT molecules.id, molecules.canonical_smiles
+            FROM molecules
+            INNER JOIN entries ON entries.molecule_id = molecules.id
+            INNER JOIN properties ON properties.molecule_id = molecules.id
+        '.$conditions.'
             ORDER BY molecules.id
         ';
 
-        $molecules = DB::select($sql, [$collection_id]);
+        $molecules = DB::select($sql, $bindings);
 
         $totalCount = count($molecules);
         if ($totalCount === 0) {
-            Log::info("No molecules found to classify in collection {$collection_id}.");
+            Log::info("No molecules found to classify in {$collectionLabel}.");
 
             return 0;
         }
 
-        Log::info("Starting NPClassifier for {$totalCount} molecules in collection {$collection_id}");
+        Log::info("Starting NPClassifier for {$totalCount} molecules in {$collectionLabel}");
 
         // Chunk the results manually
         $chunks = array_chunk($molecules, 1000);
@@ -72,23 +98,23 @@ public function handle()
             $moleculeIds = array_map(fn ($row) => $row->id, $chunk);
             $moleculeCount = count($moleculeIds);
 
-            Log::info("Processing batch of {$moleculeCount} molecules for classification in collection {$collection_id}");
+            Log::info("Processing batch of {$moleculeCount} molecules for classification in {$collectionLabel}");
 
             $batchJobs = [];
             $batchJobs[] = new ClassifyMoleculeBatch($moleculeIds);
 
             Bus::batch($batchJobs)
-                ->catch(function (Batch $batch, Throwable $e) use ($collection_id) {
-                    Log::error("NPClassifier batch failed for collection {$collection_id}: ".$e->getMessage());
+                ->catch(function (Batch $batch, Throwable $e) use ($collectionLabel) {
+                    Log::error("NPClassifier batch failed for {$collectionLabel}: ".$e->getMessage());
                 })
-                ->name("NPClassifier Batch Auto Collection {$collection_id}")
+                ->name('NPClassifier Batch Auto '.ucfirst($collectionLabel))
                 ->allowFailures()
                 ->onConnection('redis')
                 ->onQueue('default')
                 ->dispatch();
         }
 
-        Log::info("All classification jobs have been dispatched for collection {$collection_id}!");
+        Log::info("All classification jobs have been dispatched for {$collectionLabel}!");
 
         return 0;
     }

diff --git a/app/Console/Commands/SubmissionsAutoProcess/FetchCASNumbersAuto.php b/app/Console/Commands/SubmissionsAutoProcess/FetchCASNumbersAuto.php
@@ -17,7 +17,7 @@ class FetchCASNumbersAuto extends Command
      *
      * @var string
      */
-    protected $signature = 'coconut:fetch-cas-numbers {collection_id? : The ID of the collection to fetch CAS numbers for}';
+    protected $signature = 'coconut:fetch-cas-numbers {collection_id? : The ID of the collection to fetch CAS numbers for} {--all : Process all collections}';
 
     /**
      * The console command description.
@@ -40,6 +40,13 @@ public function handle()
     {
         $collection_id = $this->argument('collection_id');
 
+        if (! $collection_id && ! $this->option('all')) {
+            Log::error('Please specify either a collection_id or use --all flag');
+            $this->error('Please specify either a collection_id or use --all flag');
+
+            return 1;
+        }
+
         if ($collection_id) {
             $collection = Collection::find($collection_id);
             if (! $collection) {

diff --git a/app/Console/Commands/SubmissionsAutoProcess/GenerateCoordinates.php b/app/Console/Commands/SubmissionsAutoProcess/GenerateCoordinates.php
@@ -15,7 +15,7 @@ class GenerateCoordinates extends Command
      *
      * @var string
      */
-    protected $signature = 'coconut:generate-coordinates-auto {collection_id?}';
+    protected $signature = 'coconut:generate-coordinates-auto {collection_id?} {--all : Process all collections}';
 
     /**
      * The console command description.
@@ -31,6 +31,12 @@ public function handle()
     {
         $collectionId = $this->argument('collection_id');
 
+        if (! $collectionId && ! $this->option('all')) {
+            Log::error('Please specify either a collection_id or use --all flag');
+
+            return 1;
+        }
+
         $scriptPath = app_path('Scripts/generate_coordinates.py');
         $tmpCsv = storage_path('app/public/coordinates_input'.($collectionId ? '_'.$collectionId : '').'.csv');
         $outputJson = 'coordinates'.($collectionId ? '_'.$collectionId : '').'.json';

diff --git a/app/Console/Commands/SubmissionsAutoProcess/GenerateProperties.php b/app/Console/Commands/SubmissionsAutoProcess/GenerateProperties.php
@@ -15,7 +15,7 @@ class GenerateProperties extends Command
      *
      * @var string
      */
-    protected $signature = 'coconut:generate-properties-auto {collection_id?}';
+    protected $signature = 'coconut:generate-properties-auto {collection_id?} {--all : Process all collections}';
 
     /**
      * The console command description.
@@ -31,6 +31,12 @@ public function handle()
     {
         $collectionId = $this->argument('collection_id');
 
+        if (! $collectionId && ! $this->option('all')) {
+            Log::error('Please specify either a collection_id or use --all flag');
+
+            return 1;
+        }
+
         $outputTSV = 'properties'.($collectionId ? '_'.$collectionId : '').'.tsv';
         $scriptPath = app_path('Scripts/generate_properties.py');
 

diff --git a/app/Console/Commands/SubmissionsAutoProcess/ImportPubChemNamesAuto.php b/app/Console/Commands/SubmissionsAutoProcess/ImportPubChemNamesAuto.php
@@ -18,7 +18,7 @@ class ImportPubChemNamesAuto extends Command
      *
      * @var string
      */
-    protected $signature = 'coconut:import-pubchem-data {collection_id : The ID of the collection to process} {--retry-failed : Retry previously failed entries}';
+    protected $signature = 'coconut:import-pubchem-data {collection_id? : The ID of the collection to process} {--all : Process all collections} {--retry-failed : Retry previously failed entries}';
 
     /**
      * The console command description.
@@ -35,15 +35,24 @@ public function handle()
         $collection_id = $this->argument('collection_id');
         $retryFailed = $this->option('retry-failed');
 
-        $collection = Collection::find($collection_id);
-        if (! $collection) {
-            Log::error("Collection with ID {$collection_id} not found.");
+        if (! $collection_id && ! $this->option('all')) {
+            Log::error('Please specify either a collection_id or use --all flag');
 
             return 1;
         }
+
+        if ($collection_id !== null) {
+            $collection = Collection::find($collection_id);
+            if (! $collection) {
+                Log::error("Collection with ID {$collection_id} not found.");
+
+                return 1;
+            }
+        }
+
         $query = Molecule::select('molecules.id')
             ->join('entries', 'entries.molecule_id', '=', 'molecules.id')
-            ->where('entries.collection_id', $collection_id)
+            ->when($collection_id !== null, fn ($q) => $q->where('entries.collection_id', $collection_id))
             ->where(function ($query) {
                 $query->whereNull('molecules.name')
                     ->orWhere('molecules.name', '=', '');
@@ -67,36 +76,38 @@ public function handle()
         }
 
         // Count the total number of molecules to process
+        $collectionLabel = $collection_id !== null ? "collection {$collection_id}" : 'all collections';
+
         $totalCount = $query->count();
         if ($totalCount === 0) {
-            Log::info("No molecules found that require PubChem data import for collection {$collection_id}.");
+            Log::info("No molecules found that require PubChem data import for {$collectionLabel}.");
 
             return 0;
         }
 
-        Log::info("Starting PubChem data import for {$totalCount} molecules in collection {$collection_id}.");
+        Log::info("Starting PubChem data import for {$totalCount} molecules in {$collectionLabel}.");
 
         // Use chunk to process large sets of molecules
-        $query->chunkById(10000, function ($mols) use ($collection_id) {
+        $query->chunkById(10000, function ($mols) use ($collectionLabel) {
             $moleculeCount = count($mols);
-            Log::info("Processing batch of {$moleculeCount} molecules for collection {$collection_id}");
+            Log::info("Processing batch of {$moleculeCount} molecules for {$collectionLabel}");
 
             // Prepare batch jobs
             $batchJobs = [];
             $batchJobs[] = new ImportPubChemBatch($mols->pluck('id')->toArray());
 
             // Dispatch as a batch
             Bus::batch($batchJobs)
-                ->catch(function (Batch $batch, Throwable $e) use ($collection_id) {
-                    Log::error("PubChem import batch failed for collection {$collection_id}: ".$e->getMessage());
+                ->catch(function (Batch $batch, Throwable $e) use ($collectionLabel) {
+                    Log::error("PubChem import batch failed for {$collectionLabel}: ".$e->getMessage());
                 })
-                ->name("Import PubChem Auto Batch Collection {$collection_id}")
+                ->name('Import PubChem Auto Batch '.ucfirst($collectionLabel))
                 ->allowFailures()
                 ->onConnection('redis')
                 ->onQueue('default')
                 ->dispatch();
-        });
+        }, 'molecules.id', 'id');
 
-        Log::info("All PubChem import jobs dispatched for collection {$collection_id}!");
+        Log::info("All PubChem import jobs dispatched for {$collectionLabel}!");
     }
 }
diff --git a/app/Jobs/ImportPubChemAuto.php b/app/Jobs/ImportPubChemAuto.php
@@ -11,6 +11,7 @@
 use Illuminate\Queue\SerializesModels;
 use Illuminate\Support\Facades\Http;
 use Illuminate\Support\Facades\Log;
+use Illuminate\Support\Facades\Redis;
 
 class ImportPubChemAuto implements ShouldBeUnique, ShouldQueue
 {
@@ -30,6 +31,20 @@ class ImportPubChemAuto implements ShouldBeUnique, ShouldQueue
      */
     public $timeout = 120;
 
+    /**
+     * The number of times the job may be attempted.
+     *
+     * @var int
+     */
+    public $tries = 3;
+
+    /**
+     * The number of seconds to wait before retrying the job.
+     *
+     * @var array
+     */
+    public $backoff = [30, 60];
+
     /**
      * Create a new job instance.
      */
@@ -76,6 +91,14 @@ public function handle(): void
                     'batch_id' => $this->batch()?->id,
                 ]);
             }
+        } catch (\Illuminate\Http\Client\ConnectionException $e) {
+            // Transient network error — release back to queue for retry
+            Log::warning('PubChem connection timeout, will retry', [
+                'molecule_id' => $this->molecule->id,
+                'attempt' => $this->attempts(),
+                'error_message' => $e->getMessage(),
+            ]);
+            throw $e;
         } catch (\Throwable $e) {
             // Only actual system errors should be treated as job failures
             updateCurationStatus($this->molecule->id, $this->stepName, 'failed', $e->getMessage());
@@ -122,14 +145,23 @@ public function failed(\Throwable $exception): void
     }
 
     /**
-     * Make a throttled HTTP GET request and sleep for 200ms afterward.
+     * Make a throttled HTTP GET request, respecting a global 5 req/s limit
+     * enforced via Redis across all workers.
      */
     private function throttledGet(string $url)
     {
-        $response = Http::get($url);
-        usleep(200000); // Sleep for 200 milliseconds to limit to 5 requests per second
-
-        return $response;
+        while (true) {
+            try {
+                return Redis::throttle('pubchem-api')
+                    ->allow(5)
+                    ->every(1)
+                    ->block(0)
+                    ->then(fn () => Http::timeout(30)->connectTimeout(10)->get($url));
+            } catch (\Illuminate\Contracts\Redis\LimiterTimeoutException $e) {
+                // No slot available yet; wait 200ms before trying again
+                usleep(200000);
+            }
+        }
     }
 
     public function fetchIUPACNameFromPubChem()

diff --git a/app/Jobs/ImportPubChemBatch.php b/app/Jobs/ImportPubChemBatch.php
@@ -9,7 +9,6 @@
 use Illuminate\Foundation\Bus\Dispatchable;
 use Illuminate\Queue\InteractsWithQueue;
 use Illuminate\Queue\SerializesModels;
-use Illuminate\Support\Facades\Log;
 
 class ImportPubChemBatch implements ShouldQueue
 {
@@ -39,7 +38,6 @@ public function handle(): void
 
         $batchJobs = [];
         foreach ($molecules as $molecule) {
-            Log::info('Importing PubChem data for molecule ID: '.$molecule->id);
             array_push($batchJobs, new ImportPubChemAuto($molecule));
         }
         $this->batch()->add($batchJobs);