Fix/snapshot error handling

.env.example

@@ -73,6 +73,9 @@ BROADCAST_CONNECTION=log
 CACHE_STORE=file
 QUEUE_CONNECTION=redis
 
+# Horizon workers start automatically with Sail (see docker/8.4/supervisord.conf).
+# After changing queue/redis settings, run: ./vendor/bin/sail artisan horizon:terminate
+
 SESSION_DRIVER=redis
 SESSION_LIFETIME=120
 SESSION_ENCRYPT=false

app/Actions/Project/AddProjectMember.php

@@ -47,7 +47,7 @@ protected function validate($project, string $email, ?string $role)
             'email' => $email,
             'role' => $role,
         ], $this->rules(), [
-            'email.exists' => __('We were unable to find a registered user with this email address.'),
+            'email.exists' => __('Unable to add member with this email address.'),
         ])->after(
             $this->ensureUserIsNotAlreadyOnProject($project, $email)
         )->validateWithBag('addModelMember');
@@ -80,7 +80,7 @@ protected function ensureUserIsNotAlreadyOnProject($project, string $email)
             $validator->errors()->addIf(
                 $project->hasUserWithEmail($email),
                 'email',
-                __('This user already belongs to the project.')
+                __('Unable to add member with this email address.')
             );
         };
     }

app/Actions/Project/InviteProjectMember.php

@@ -24,7 +24,7 @@ class InviteProjectMember
      */
     public function invite($user, $project, string $email, ?string $role = null, ?string $message = null)
     {
-        // Gate::forUser($user)->authorize('addProjectMember', $project);
+        Gate::forUser($user)->authorize('addProjectMember', $project);
 
         $this->validate($project, $email, $role, $message);
 

app/Console/Commands/RefreshNmriumInfo.php

@@ -5,6 +5,7 @@
 use App\Http\Controllers\StudyController;
 use App\Models\Study;
 use App\Support\Nmr\JcampDatasetClassifier;
+use App\Support\Nmr\NmriumSpectraInfoInspector;
 use Illuminate\Console\Command;
 use Illuminate\Support\Facades\Http;
 use Illuminate\Support\Facades\Log;
@@ -75,7 +76,7 @@ public function handle(): int
             }
 
             $jcampBackfilled = $this->backfillUnparsedJcampDatasets($study);
-            if (! $this->needsRefresh($spectra)) {
+            if (! NmriumSpectraInfoInspector::needsRefresh($spectra)) {
                 if ($jcampBackfilled > 0) {
                     $this->info(sprintf('study %d %s — info OK; classified %d JCAMP-only file(s)', $study->id, $study->name, $jcampBackfilled));
                     $touched++;
@@ -237,32 +238,6 @@ protected function spectrumKey(array $spectrum): ?string
         return null;
     }
 
-    /**
-     * Heuristically decide whether at least one spectrum in the stored
-     * payload is missing real metadata. We treat `info` as "needs refresh"
-     * when it is empty, missing the `experiment` key, or has been corrupted
-     * with raw `{im, re}` payloads from the legacy SpectraEditor bug.
-     *
-     * @param  array<int, array<string, mixed>>  $spectra
-     */
-    protected function needsRefresh(array $spectra): bool
-    {
-        foreach ($spectra as $spec) {
-            $info = $spec['info'] ?? null;
-            if (! is_array($info) || empty($info)) {
-                return true;
-            }
-            if (isset($info['im']) || isset($info['re'])) {
-                return true;
-            }
-            if (! array_key_exists('experiment', $info) && ! array_key_exists('nucleus', $info)) {
-                return true;
-            }
-        }
-
-        return false;
-    }
-
     /**
      * Re-derive `dataset.type` for every dataset of the study using the same
      * spectrum-to-dataset matching the controller does on save.

app/Console/Commands/RepairMissingCompoundInfoCommand.php

@@ -0,0 +1,88 @@
+<?php
+
+namespace App\Console\Commands;
+
+use App\Support\Molecules\MoleculeEnrichmentInspector;
+use App\Support\Nmr\NmriumSpectraInfoInspector;
+use Illuminate\Console\Command;
+use Illuminate\Support\Facades\Artisan;
+
+class RepairMissingCompoundInfoCommand extends Command
+{
+    protected $signature = 'nmrxiv:repair-missing-compound-info
+                            {--molecule-limit=10 : Max molecules to enrich per run}
+                            {--nmrium : Only repair NMRium spectrum metadata}
+                            {--molecules : Only enrich molecule records}';
+
+    protected $description = 'Detect missing compound / spectrum metadata and run the appropriate repair commands';
+
+    public function handle(): int
+    {
+        $onlyNmrium = (bool) $this->option('nmrium');
+        $onlyMolecules = (bool) $this->option('molecules');
+        $runBoth = ! $onlyNmrium && ! $onlyMolecules;
+
+        $exitCode = self::SUCCESS;
+
+        if ($runBoth || $onlyMolecules) {
+            $exitCode = max($exitCode, $this->repairMoleculesIfNeeded());
+        }
+
+        if ($runBoth || $onlyNmrium) {
+            $exitCode = max($exitCode, $this->repairNmriumIfNeeded());
+        }
+
+        return $exitCode;
+    }
+
+    protected function repairMoleculesIfNeeded(): int
+    {
+        $pending = MoleculeEnrichmentInspector::needingEnrichmentQuery()->count();
+
+        if ($pending === 0) {
+            $this->line('No molecules with missing compound metadata.');
+
+            return self::SUCCESS;
+        }
+
+        $limit = max(1, (int) $this->option('molecule-limit'));
+
+        $this->info(sprintf(
+            'Found %d molecule(s) with missing compound metadata; enriching up to %d.',
+            $pending,
+            min($pending, $limit)
+        ));
+
+        return Artisan::call('nmrxiv:molecules-clean', [
+            '--force' => true,
+            '--limit' => min($pending, $limit),
+        ], $this->output);
+    }
+
+    protected function repairNmriumIfNeeded(): int
+    {
+        if (rtrim((string) config('external-links.nmrkit_url'), '/') === '') {
+            $this->warn('NMRKIT_URL is not configured; skipping NMRium metadata repair.');
+
+            return self::SUCCESS;
+        }
+
+        [$studyId, $pending] = NmriumSpectraInfoInspector::firstStudyNeedingRefresh();
+
+        if ($pending === 0) {
+            $this->line('No studies with missing NMRium spectrum metadata.');
+
+            return self::SUCCESS;
+        }
+
+        $this->info(sprintf(
+            'Found %d study/studies with missing NMRium spectrum metadata; refreshing study %d.',
+            $pending,
+            $studyId
+        ));
+
+        return Artisan::call('nmrxiv:refresh-nmrium-info', [
+            '--study' => $studyId,
+        ], $this->output);
+    }
+}

app/Http/Controllers/API/Auth/LoginController.php

@@ -174,8 +174,8 @@ public function login(Request $request): JsonResponse
 
         if (! $user->hasVerifiedEmail()) {
             return response()->json([
-                'message' => 'Account is not yet verified. Please verify your email address by clicking on the link we just emailed to you.',
-            ], 403);
+                'message' => 'Invalid login details',
+            ], 401);
         }
 
         $token = $user->createToken('auth_token')->plainTextToken;