fix(draft): reuse the study-backed project when drafts have duplicate rows

app/Actions/Draft/FindOrCreateDraftStudy.php

@@ -25,6 +25,8 @@ public function execute(FileSystemObject $folder, Draft $draft, Project $project
         if (! $study) {
             $study = $this->createNewStudy($folder, $draft, $project, $validation);
             $this->updateFolderWithStudy($folder, $study);
+        } else {
+            $this->reassignStudyToProject($study, $project);
         }
 
         return $study;
@@ -66,4 +68,20 @@ private function updateFolderWithStudy(FileSystemObject $folder, Study $study):
         $folder->study_id = $study->id;
         $folder->save();
     }
+
+    /**
+     * Keep an existing study on the project this process run is using.
+     */
+    private function reassignStudyToProject(Study $study, Project $project): void
+    {
+        if ($study->project_id === $project->id) {
+            return;
+        }
+
+        $study->project_id = $project->id;
+        $study->save();
+
+        $study->sample()->update(['project_id' => $project->id]);
+        $study->datasets()->update(['project_id' => $project->id]);
+    }
 }

app/Actions/Draft/ProcessDraft.php

@@ -15,7 +15,6 @@
 use App\Models\Validation;
 use App\Support\Draft\HifsaPdfResolver;
 use Illuminate\Http\JsonResponse;
-use Illuminate\Http\RedirectResponse;
 use Illuminate\Http\Request;
 use Illuminate\Http\Response;
 use Illuminate\Support\Facades\DB;
@@ -36,7 +35,7 @@ public function __construct(
     /**
      * Process draft and create project structure.
      */
-    public function execute(Request $request, Draft $draft, User $user): Response|JsonResponse|RedirectResponse
+    public function execute(Request $request, Draft $draft, User $user): Response|JsonResponse
     {
         [$user_id, $team_id, $team] = $user->getUserTeamData();
 
@@ -94,7 +93,7 @@ private function prepareDraft(Request $request, Draft $draft): void
      */
     public function createOrUpdateProject(Draft $draft, int $user_id, int $team_id, $user, $team): Project
     {
-        $project = Project::where('draft_id', $draft->id)->first();
+        $project = $this->resolveDraftProject($draft);
 
         if (! $project) {
             $project = $this->createNewProject($draft, $user_id, $team_id, $user, $team);
@@ -105,6 +104,40 @@ public function createOrUpdateProject(Draft $draft, int $user_id, int $team_id,
         return $project;
     }
 
+    /**
+     * Pick the existing project for this draft.
+     *
+     * A draft can accumulate more than one project row (retries, concurrent
+     * process requests). `first()` without an order then often returns an
+     * empty newer project while studies still belong to an older one, so
+     * finalizeProcessing sees zero studies and redirects.
+     */
+    public function resolveDraftProject(Draft $draft): ?Project
+    {
+        $studyProjectId = Study::query()
+            ->where('draft_id', $draft->id)
+            ->whereNotNull('project_id')
+            ->value('project_id');
+
+        if ($studyProjectId) {
+            $project = Project::query()->find($studyProjectId);
+
+            if ($project) {
+                if ($project->draft_id !== $draft->id) {
+                    $project->draft_id = $draft->id;
+                    $project->save();
+                }
+
+                return $project;
+            }
+        }
+
+        return Project::query()
+            ->where('draft_id', $draft->id)
+            ->orderBy('id')
+            ->first();
+    }
+
     /**
      * Create a new project from draft.
      */
@@ -363,16 +396,23 @@ public function createDatasetFromOrphanedFile(FileSystemObject $folder, Study $s
     /**
      * Finalize processing and return response.
      */
-    public function finalizeProcessing(Draft $draft, Project $project): Response|JsonResponse|RedirectResponse
+    public function finalizeProcessing(Draft $draft, Project $project): Response|JsonResponse
     {
         $draft->save();
 
         $studies = $project->studies()->orderBy('name')->get()->load(['datasets', 'sample.molecules', 'tags']);
         $this->hifsaPdfResolver->persistCsvData($studies);
         $studies = $this->hifsaPdfResolver->enrichStudies($studies, $draft);
 
-        if (count($studies) == 0) {
-            return redirect()->back()->withErrors(['studies' => 'nmrXiv requires raw or processed raw instrument output files. If you data is from a single sample organise all the files in one folder and click proceed. If you have multiple samples, group your data in subfolders with each subfolder corresponding to a sample. Thank you.']);
+        if ($studies->isEmpty()) {
+            $message = 'nmrXiv requires raw or processed raw instrument output files. If you data is from a single sample organise all the files in one folder and click proceed. If you have multiple samples, group your data in subfolders with each subfolder corresponding to a sample. Thank you.';
+
+            return response()->json([
+                'message' => $message,
+                'errors' => [
+                    'studies' => [$message],
+                ],
+            ], 422);
         }
 
         Log::info('Finalizing processing for draft '.$draft->id);

app/Actions/Project/PublishEmbargoProject.php

@@ -103,7 +103,7 @@ private function validateForPublication(Project $project, bool $restoreReleaseDa
         $project->release_date = now()->startOfDay()->toDateString();
         $project->save();
 
-        $validation->process();
+        $validation->process(project: $project);
         $publishAttemptValidation = $validation->fresh();
 
         if (! $publishAttemptValidation['report']['project']['status']) {
@@ -113,7 +113,7 @@ private function validateForPublication(Project $project, bool $restoreReleaseDa
                 $project->refresh();
 
                 if ($project->validation) {
-                    $project->validation->process();
+                    $project->validation->process(project: $project);
                 }
             }
 

app/Actions/Project/UpdateProject.php

@@ -149,7 +149,7 @@ public function update(Project $project, array $input)
                     }
                 }
             }
-            $validation->process();
+            $validation->process(project: $project);
 
             $project = $project->fresh();
 

app/Http/Controllers/DraftController.php

@@ -16,7 +16,6 @@
 use App\Support\ProvisionalDoi;
 use Illuminate\Database\Eloquent\Collection;
 use Illuminate\Http\JsonResponse;
-use Illuminate\Http\RedirectResponse;
 use Illuminate\Http\Request;
 use Illuminate\Http\Response;
 use Illuminate\Support\Facades\Auth;
@@ -67,10 +66,8 @@ public function all(Request $request): JsonResponse
 
     /**
      * Process draft and convert to project structure.
-     *
-     * @return Response|JsonResponse|RedirectResponse
      */
-    public function process(Request $request, Draft $draft)
+    public function process(Request $request, Draft $draft): Response|JsonResponse
     {
         $this->authorize('updateDraft', $draft);
 
@@ -176,7 +173,7 @@ public function complete(Request $request, Draft $draft): JsonResponse
     {
         $this->authorize('updateDraft', $draft);
 
-        $project = Project::where('draft_id', $draft->id)->first();
+        $project = $this->processDraft->resolveDraftProject($draft);
 
         if (! $project) {
             return response()->json([
@@ -186,10 +183,12 @@ public function complete(Request $request, Draft $draft): JsonResponse
         }
 
         $validation = $project->validation;
-        $validation->process();
+        $validation->process(project: $project);
+
+        $project->load(['studies.datasets', 'owner', 'citations', 'authors', 'tags']);
 
         return response()->json([
-            'project' => Project::with(['studies.datasets', 'owner', 'citations', 'authors', 'tags'])->where('draft_id', $draft->id)->first(),
+            'project' => $project,
             'validation' => $validation,
         ]);
     }
@@ -201,7 +200,7 @@ public function info(Request $request, Draft $draft): JsonResponse
     {
         $this->authorize('updateDraft', $draft);
 
-        $project = Project::where('draft_id', $draft->id)->first();
+        $project = $this->processDraft->resolveDraftProject($draft);
 
         if (! $project) {
             return response()->json([
@@ -268,7 +267,7 @@ public function status(Request $request, Draft $draft): JsonResponse
     {
         $this->authorize('updateDraft', $draft);
 
-        $project = Project::where('draft_id', $draft->id)->first();
+        $project = $this->processDraft->resolveDraftProject($draft);
 
         if (! $project) {
             return response()->json([
@@ -321,7 +320,7 @@ public function storeProvisionalDoi(Request $request, Draft $draft): JsonRespons
             $payload = DB::transaction(function () use ($draft, $user, $user_id, $team_id, $team): array {
                 Draft::query()->whereKey($draft->id)->lockForUpdate()->firstOrFail();
 
-                $project = Project::query()->where('draft_id', $draft->id)->first();
+                $project = $this->processDraft->resolveDraftProject($draft);
 
                 if (! $project) {
                     $project = $this->processDraft->createNewProject($draft, $user_id, $team_id, $user, $team);
@@ -357,7 +356,7 @@ public function destroyProvisionalDoi(Request $request, Draft $draft): Response
     {
         $this->authorize('updateDraft', $draft);
 
-        $project = Project::query()->where('draft_id', $draft->id)->first();
+        $project = $this->processDraft->resolveDraftProject($draft);
 
         if (! $project) {
             return response()->noContent();

app/Http/Controllers/ProjectController.php

@@ -349,7 +349,7 @@ public function validation(Request $request, Project $project)
             }
         }
 
-        $validation->process();
+        $validation->process(project: $project);
 
         return Inertia::render('Project/Validation', [
             'project' => $project->load('projectInvitations', 'tags', 'authors', 'citations', 'fundingReferences'),
@@ -377,7 +377,7 @@ public function validationReport(Request $request, Project $project)
             }
         }
 
-        $validation->process();
+        $validation->process(project: $project);
 
         return $validation->fresh();
     }
@@ -409,7 +409,7 @@ public function publish(Request $request, Project $project, PublishProject $publ
                 }
 
                 $project->release_date = $request->get('release_date');
-                $validation->process();
+                $validation->process(project: $project);
                 $validation = $validation->fresh();
                 if ($validation['report']['project']['status']) {
                     $project->status = 'queued';
@@ -467,7 +467,7 @@ public function publish(Request $request, Project $project, PublishProject $publ
 
                 $validation = $project->validation;
                 if ($validation) {
-                    $validation->process(forceSamplesMode: true);
+                    $validation->process(forceSamplesMode: true, project: $project);
                     $validation = $validation->fresh();
                 }
 
@@ -562,7 +562,7 @@ protected function publishValidationHintsFromReport(?array $report): array
 
         $citations = $project['citations'] ?? null;
         if (is_string($citations) && str_starts_with($citations, 'false|')) {
-            $hints[] = 'Add a DOI to every citation, or choose a future release date if you are not ready to publish immediately.';
+            $hints[] = 'Add at least one citation before publishing in project mode.';
         }
 
         $labels = [

app/Http/Controllers/UploadController.php

@@ -2,8 +2,8 @@
 
 namespace App\Http\Controllers;
 
+use App\Actions\Draft\ProcessDraft;
 use App\Models\Draft;
-use App\Models\Project;
 use Illuminate\Auth\Access\AuthorizationException;
 use Illuminate\Http\Request;
 use Illuminate\Support\Facades\Auth;
@@ -12,6 +12,8 @@
 
 class UploadController extends Controller
 {
+    public function __construct(private ProcessDraft $processDraft) {}
+
     public function upload(Request $request)
     {
         $draftId = $request->get('draft_id');
@@ -20,7 +22,7 @@ public function upload(Request $request)
             $draft = Draft::find((int) $draftId);
 
             if ($draft && $request->user()?->can('updateDraft', $draft)) {
-                $project = Project::where('draft_id', $draft->id)->first();
+                $project = $this->processDraft->resolveDraftProject($draft);
 
                 if ($project && $project->status !== 'draft') {
                     return redirect()->route('publish', ['draft' => $draft->id]);
@@ -39,7 +41,7 @@ public function publish(Request $request, Draft $draft)
     {
         $this->authorize('updateDraft', $draft);
 
-        $project = Project::where('draft_id', $draft->id)->first();
+        $project = $this->processDraft->resolveDraftProject($draft);
 
         if (! $project) {
             return redirect()->route('upload', ['draft_id' => $draft->id]);
@@ -50,11 +52,23 @@ public function publish(Request $request, Draft $draft)
         }
 
         $validation = $project->validation;
-        $validation->process();
+        $validation->process(project: $project);
+
+        $project->load([
+            'studies.datasets',
+            'studies.sample.molecules',
+            'studies.sample.mixtureComposition.components.molecule',
+            'owner',
+            'citations',
+            'fundingReferences',
+            'authors',
+            'tags',
+            'license',
+        ]);
 
         return Inertia::render('Publish', [
             'draft' => $draft,
-            'project' => Project::with(['studies.datasets', 'studies.sample.molecules', 'studies.sample.mixtureComposition.components.molecule', 'owner', 'citations', 'fundingReferences', 'authors', 'tags', 'license'])->where('draft_id', $draft->id)->first(),
+            'project' => $project,
             'validation' => $validation,
         ]);
     }

app/Jobs/ProcessFiles.php

@@ -2,9 +2,9 @@
 
 namespace App\Jobs;
 
+use App\Actions\Draft\ProcessDraft;
 use App\Models\Draft;
 use App\Models\FileSystemObject;
-use App\Models\Project;
 use Illuminate\Bus\Queueable;
 use Illuminate\Contracts\Queue\ShouldBeUnique;
 use Illuminate\Contracts\Queue\ShouldQueue;
@@ -119,7 +119,7 @@ private function updateFileSystemObjectStatus(FileSystemObject $fsObject): bool
      */
     private function handleMissingFilesRestored(): void
     {
-        $project = Project::where('draft_id', $this->draft->id)->first();
+        $project = app(ProcessDraft::class)->resolveDraftProject($this->draft);
 
         if (! $project) {
             Log::warning('No project found for draft '.$this->draft->id);

app/Jobs/ValidateAndSubmitELNDraft.php

@@ -76,7 +76,7 @@ public function handle(): void
 
             // Process validation
             $validation = $project->validation;
-            $validation->process();
+            $validation->process(project: $project);
             $validation = $validation->fresh();
 
             $status = true;