Development

.env.ci.test

@@ -25,8 +25,8 @@ DB_DATABASE=nmrxiv
 DB_USERNAME=postgres
 DB_PASSWORD=postgres
 
-BROADCAST_DRIVER=log
-CACHE_DRIVER=file
+BROADCAST_CONNECTION=log
+CACHE_STORE=file
 FILESYSTEM_DRIVER=local
 QUEUE_CONNECTION=redis
 SESSION_DRIVER=redis
@@ -44,7 +44,7 @@ MAIL_HOST=mailhog
 MAIL_PORT=1025
 MAIL_USERNAME=null
 MAIL_PASSWORD=null
-MAIL_ENCRYPTION=null
+MAIL_SCHEME=null
 MAIL_FROM_ADDRESS=info@nmrxiv.org
 MAIL_FROM_NAME="${APP_NAME}"
 

.env.example

@@ -3,6 +3,15 @@ APP_ENV=local
 APP_KEY=
 APP_DEBUG=true
 APP_URL=http://localhost:80
+
+APP_LOCALE=en
+APP_FALLBACK_LOCALE=en
+APP_FAKER_LOCALE=en_US
+APP_MAINTENANCE_DRIVER=file
+APP_MAINTENANCE_STORE=database
+PHP_CLI_SERVER_WORKERS=4
+
+BCRYPT_ROUNDS=12
 APP_DESCRIPTION='nmrXiv is currently developed as the FAIR, consensus-driven NMR data repository and computational platform. The ultimate goal is to accelerate broader coordination and data sharing among natural product (NP) researchers by enabling the storage, management, sharing and analysis of NMR data.'
 COOL_OFF_PERIOD=10
 SCHEMA_VERSION=beta
@@ -20,6 +29,7 @@ DATACITE_API=https://api.datacite.org/
 
 
 LOG_CHANNEL=stack
+LOG_STACK=single
 LOG_LEVEL=debug
 
 DB_CONNECTION=pgsql
@@ -29,12 +39,15 @@ DB_DATABASE=nmrxiv
 DB_USERNAME=sail
 DB_PASSWORD=password
 
-BROADCAST_DRIVER=log
-CACHE_DRIVER=file
+BROADCAST_CONNECTION=log
+CACHE_STORE=file
 FILESYSTEM_DRIVER=local
 QUEUE_CONNECTION=redis
 SESSION_DRIVER=redis
 SESSION_LIFETIME=120
+SESSION_ENCRYPT=false
+SESSION_PATH=/
+SESSION_DOMAIN=null
 
 MEMCACHED_HOST=memcached
 
@@ -48,7 +61,7 @@ MAIL_HOST=mailhog
 MAIL_PORT=1025
 MAIL_USERNAME=null
 MAIL_PASSWORD=null
-MAIL_ENCRYPTION=null
+MAIL_SCHEME=null
 MAIL_FROM_ADDRESS=info.nmrxiv@uni-jena.de
 MAIL_FROM_NAME="${APP_NAME}"
 

.github/workflows/deploy-docs.yml

@@ -1,33 +1,64 @@
 name: Docs Deployment - GitHub pages
+
 on:
-  workflow_dispatch: {}
+  # Runs on pushes targeting the `main` branch. Change this to `master` if you're
+  # using the `master` branch as the default branch.
   push:
-    branches:
-      - development
+    branches: [development]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
 jobs:
-  deploy:
+  # Build job
+  build:
     runs-on: ubuntu-latest
-    permissions:
-      pages: write
-      id-token: write
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
     steps:
-      - uses: actions/checkout@v4
+      - name: Checkout
+        uses: actions/checkout@v4
         with:
-          fetch-depth: 0
-      - uses: actions/setup-node@v4
+          fetch-depth: 0 # Not needed if lastUpdated is not enabled
+      # - uses: pnpm/action-setup@v3 # Uncomment this block if you're using pnpm
+      #   with:
+      #     version: 9 # Not needed if you've set "packageManager" in package.json
+      # - uses: oven-sh/setup-bun@v1 # Uncomment this if you're using Bun
+      - name: Setup Node
+        uses: actions/setup-node@v4
         with:
           node-version: 20
-          cache: npm
-      - run: npm ci
-      - name: Build
-        run: npm run docs:build
-      - uses: actions/configure-pages@v5
-      - uses: actions/upload-pages-artifact@v3
+          cache: npm # or pnpm / yarn
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+      - name: Install dependencies
+        run: npm ci # or pnpm install / yarn install / bun install
+      - name: Build with VitePress
+        run: npm run docs:build # or pnpm docs:build / yarn docs:build / bun run docs:build
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
         with:
           path: docs/.vitepress/dist
-      - name: Deploy
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    needs: build
+    runs-on: ubuntu-latest
+    name: Deploy
+    steps:
+      - name: Deploy to GitHub Pages
         id: deployment
         uses: actions/deploy-pages@v4

.gitignore

@@ -3,6 +3,7 @@
 /public/build
 /public/storage
 /storage/*.key
+/storage/pail
 /vendor
 .env
 .env.backup
@@ -13,6 +14,7 @@ Homestead.yaml
 npm-debug.log
 yarn-error.log
 /.idea
+/.nova
 /.vscode
 /resources/ops/kubernetes/secret.yml
 docs/.vitepress/dist

app/Actions/Jetstream/CreateTeam.php

@@ -31,7 +31,7 @@ public function create($user, array $input)
             'personal_team' => false,
         ]));
 
-        //return $team;
+        // return $team;
         return redirect()->route('dashboard')->with('success', 'Team created successfully');
     }
 }

app/Actions/Project/CreateNewProject.php

@@ -56,7 +56,7 @@ public function create(array $input)
                         $user, ['role' => 'creator']
                     );
                 }
-                $validaton = new Validation();
+                $validaton = new Validation;
                 $validaton->save();
                 $project->associate($validation);
                 $project->save();

app/Actions/Project/DeleteProject.php

@@ -92,14 +92,14 @@ public function deleteStudy($study)
     {
         $datasets = $study->datasets;
         $sample = $study->sample;
-        //Detach Molecules and Delete Sample
+        // Detach Molecules and Delete Sample
         if ($sample) {
             $this->deleteSample($sample);
         }
         foreach ($datasets as $dataset) {
             $this->deleteDatasets($dataset);
         }
-        //Delete Study
+        // Delete Study
         $study->delete();
     }
 
@@ -115,7 +115,7 @@ public function deleteDatasets($dataset)
         if ($nmriumInfo) {
             $this->deleteNMRium($nmriumInfo);
         }
-        //Delete Dataset
+        // Delete Dataset
         $dataset->delete();
     }
 
@@ -133,26 +133,26 @@ public function deleteProject($project)
         $draft = $project->draft;
         $validation = $project->validation;
 
-        //Detach Authors
+        // Detach Authors
         if ($authors && count($authors) > 0) {
             $project->authors()->detach(
                 $authors
             );
         }
-        //Detach Citations
+        // Detach Citations
         if ($citations && count($citations) > 0) {
             $project->citations()->detach(
                 $citations
             );
         }
-        //Delete Validations
+        // Delete Validations
         if ($validation) {
             $validation->delete();
         }
-        //Delete Project
+        // Delete Project
         $project->delete();
 
-        //Delete Draft and Files
+        // Delete Draft and Files
         if ($draft) {
             $this->deleteDraft($draft);
         }
@@ -183,12 +183,12 @@ public function deleteNMRium($nmriumInfo)
      */
     public function deleteDraft($draft)
     {
-        //Delete Files
+        // Delete Files
         $files = $draft->files;
         foreach ($files as $file) {
             $this->deleteFSO($file);
         }
-        //Delete Draft
+        // Delete Draft
         $draft = $draft->refresh();
         $draft->delete();
     }

app/Actions/Project/InviteProjectMember.php

@@ -28,7 +28,7 @@ public function invite($user, $project, string $email, ?string $role = null, ?st
 
         $this->validate($project, $email, $role, $message);
 
-        //InvitingProjectMember::dispatch($project, $email, $role, $message);
+        // InvitingProjectMember::dispatch($project, $email, $role, $message);
 
         $invitation = $project->projectInvitations()->create([
             'email' => $email,

app/Actions/Project/UpdateProject.php

@@ -107,7 +107,7 @@ public function update(Project $project, array $input)
             $validation = $project->validation;
 
             if (! $validation) {
-                $validation = new Validation();
+                $validation = new Validation;
                 $validation->save();
                 $project->validation()->associate($validation);
                 $project->save();
@@ -145,7 +145,7 @@ public function update(Project $project, array $input)
      */
     public function attachAuthor(Project $project, $authors)
     {
-        //dd($authors);
+        // dd($authors);
         $authors_map = [];
         $index = 0;
         foreach ($authors as $author) {

app/Actions/Study/InviteStudyMember.php

@@ -29,7 +29,7 @@ public function invite($user, $study, string $email, ?string $role = null, ?stri
 
         $this->validate($study, $email, $role, $message);
 
-        //InvitingStudyMember::dispatch($study, $email, $role, $message);
+        // InvitingStudyMember::dispatch($study, $email, $role, $message);
 
         $invitation = $study->studyInvitations()->create([
             'email' => $email,
@@ -43,7 +43,7 @@ public function invite($user, $study, string $email, ?string $role = null, ?stri
         $invitedUser = User::where('email', $invitation->email)->first();
 
         if ($invitedUser) {
-            //$invitedUser->notify(new StudyInviteNotification($invitation));
+            // $invitedUser->notify(new StudyInviteNotification($invitation));
             event(new StudyInvite($invitedUser, $invitation));
         }
     }

app/Console/Commands/ArchiveData.php

@@ -27,9 +27,9 @@ class ArchiveData extends Command
     /**
      * Execute the console command.
      */
-    public function handle()
+    public function handle(): void
     {
-        return DB::transaction(function () {
+        DB::transaction(function () {
             $projects = Project::where([
                 ['is_public', true],
                 ['download_url', null],

app/Console/Commands/AssignDOIs.php

@@ -26,10 +26,8 @@ class AssignDOIs extends Command
 
     /**
      * Execute the console command.
-     *
-     * @return int
      */
-    public function handle(AssignIdentifier $assigner)
+    public function handle(AssignIdentifier $assigner): int
     {
         return DB::transaction(function () use ($assigner) {
             $projects = Project::where([

app/Console/Commands/AssignIdentifiers.php

@@ -26,10 +26,8 @@ class AssignIdentifiers extends Command
 
     /**
      * Execute the console command.
-     *
-     * @return int
      */
-    public function handle(DOIService $doiService)
+    public function handle(DOIService $doiService): int
     {
         return DB::transaction(function () use ($doiService) {
             $projects = Project::where([

app/Console/Commands/DataBackup.php

@@ -24,7 +24,7 @@ class DataBackup extends Command
     /**
      * Execute the console command.
      */
-    public function handle()
+    public function handle(): void
     {
         DataBackupJob::dispatch();
     }

app/Console/Commands/DeleteAuthor.php

@@ -24,10 +24,8 @@ class DeleteAuthor extends Command
 
     /**
      * Execute the console command.
-     *
-     * @return int
      */
-    public function handle()
+    public function handle(): int
     {
         $ids = $this->argument('ids') ? explode(',', $this->argument('ids')) : null;
         if ($ids) {

app/Console/Commands/DeleteCitation.php

@@ -24,10 +24,8 @@ class DeleteCitation extends Command
 
     /**
      * Execute the console command.
-     *
-     * @return int
      */
-    public function handle()
+    public function handle(): int
     {
         $ids = $this->argument('ids') ? explode(',', $this->argument('ids')) : null;
         if ($ids) {