Apply coding style

.gitignore

@@ -19,6 +19,5 @@ npm-debug.log
 yarn-error.log
 /*.sublime-*
 /*.phar
-/*.php_cs.cache
+/*.php-cs-fixer.cache
 /.idea
-/.vscode

.php-cs-fixer.php

@@ -0,0 +1,34 @@
+<?php
+
+$finder = (new PhpCsFixer\Finder())
+    ->files()
+    ->in([
+        __DIR__.'/app',
+        __DIR__.'/tests',
+        __DIR__.'/config',
+        __DIR__.'/database',
+        // __DIR__.'/vendor/biigle',
+    ])
+    ->name('*.php')
+    ->ignoreDotFiles(true)
+    ->ignoreVCS(true);
+
+return (new PhpCsFixer\Config())
+    ->setRules([
+        '@PSR2' => true,
+        'ordered_imports' => true,
+        'single_space_around_construct' => true,
+        'array_indentation' => true,
+        'array_syntax' => ['syntax' => 'short'],
+        'combine_consecutive_unsets' => true,
+        'class_attributes_separation' => ['elements' => ['method' => 'one', ]],
+        'no_whitespace_before_comma_in_array' => true,
+        'unary_operator_spaces' => true,
+        'whitespace_after_comma_in_array' => true,
+        'method_chaining_indentation' => true,
+        'use_arrow_functions' => true,
+        'no_unused_imports' => true
+    ])
+    ->setFinder($finder)
+    ->setRiskyAllowed(true)
+    ->setUsingCache(true);

CONTRIBUTING.md

@@ -26,6 +26,6 @@ The default development setup of BIIGLE uses the `dev-modules` branch of the cor
 
 BIIGLE uses readable and meaningful commit messages. Please follow [this guide](https://chris.beams.io/posts/git-commit/) for your commits to BIIGLE.
 
-BIIGLE also defines a PHP coding style in [`.php_cs`](.php_cs). Use the [PHP CS Fixer](https://github.com/FriendsOfPHP/PHP-CS-Fixer) to apply the coding style to your source code.
+BIIGLE also defines a PHP coding style in [`.php-cs-fixer.php`](.php-cs-fixer.php). Use the [PHP CS Fixer](https://github.com/FriendsOfPHP/PHP-CS-Fixer) to apply the coding style to your source code.
 
 All changes or new features that affect the API or backend PHP code should be thoroughly tested.

app/AnnotationSession.php

@@ -93,11 +93,12 @@ public function getVolumeFileAnnotations(VolumeFile $file, User $user)
             $query->with(['labels' => function ($query) use ($user) {
                 // wrap this in a where because the default query already has a where
                 $query->where(function ($query) use ($user) {
-                    $query->where(function ($query) {
-                        $query->where('created_at', '>=', $this->starts_at)
-                            ->where('created_at', '<', $this->ends_at);
-                    })
-                    ->orWhere('user_id', '!=', $user->id);
+                    $query
+                        ->where(function ($query) {
+                            $query->where('created_at', '>=', $this->starts_at)
+                                ->where('created_at', '<', $this->ends_at);
+                        })
+                        ->orWhere('user_id', '!=', $user->id);
                 });
             }]);
         } else {
@@ -205,25 +206,26 @@ public function imageAnnotations()
     {
         return ImageAnnotation::where(function ($query) {
             // all annotations of the associated volume
-            return $query->whereIn('image_id', function ($query) {
-                $query->select('id')
+            return $query
+                ->whereIn('image_id', function ($query) {
+                    $query->select('id')
                         ->from('images')
                         ->where('volume_id', $this->volume_id);
-            })
-            // that were created between the start and end date
-            ->where('created_at', '>=', $this->starts_at)
-            ->where('created_at', '<', $this->ends_at)
-            // and have a label by one of the members of this session
-            ->whereExists(function ($query) {
-                $query->select(DB::raw(1))
-                    ->from('image_annotation_labels')
-                    ->whereRaw('image_annotation_labels.annotation_id = image_annotations.id')
-                    ->whereIn('image_annotation_labels.user_id', function ($query) {
-                        $query->select('user_id')
-                            ->from('annotation_session_user')
-                            ->where('annotation_session_id', $this->id);
-                    });
-            });
+                })
+                // that were created between the start and end date
+                ->where('created_at', '>=', $this->starts_at)
+                ->where('created_at', '<', $this->ends_at)
+                // and have a label by one of the members of this session
+                ->whereExists(function ($query) {
+                    $query->select(DB::raw(1))
+                        ->from('image_annotation_labels')
+                        ->whereRaw('image_annotation_labels.annotation_id = image_annotations.id')
+                        ->whereIn('image_annotation_labels.user_id', function ($query) {
+                            $query->select('user_id')
+                                ->from('annotation_session_user')
+                                ->where('annotation_session_id', $this->id);
+                        });
+                });
         });
     }
 
@@ -238,25 +240,26 @@ public function videoAnnotations()
     {
         return VideoAnnotation::where(function ($query) {
             // all annotations of the associated volume
-            return $query->whereIn('video_id', function ($query) {
-                $query->select('id')
+            return $query
+                ->whereIn('video_id', function ($query) {
+                    $query->select('id')
                         ->from('videos')
                         ->where('volume_id', $this->volume_id);
-            })
-            // that were created between the start and end date
-            ->where('created_at', '>=', $this->starts_at)
-            ->where('created_at', '<', $this->ends_at)
-            // and have a label by one of the members of this session
-            ->whereExists(function ($query) {
-                $query->select(DB::raw(1))
-                    ->from('video_annotation_labels')
-                    ->whereRaw('video_annotation_labels.annotation_id = video_annotations.id')
-                    ->whereIn('video_annotation_labels.user_id', function ($query) {
-                        $query->select('user_id')
-                            ->from('annotation_session_user')
-                            ->where('annotation_session_id', $this->id);
-                    });
-            });
+                })
+                // that were created between the start and end date
+                ->where('created_at', '>=', $this->starts_at)
+                ->where('created_at', '<', $this->ends_at)
+                // and have a label by one of the members of this session
+                ->whereExists(function ($query) {
+                    $query->select(DB::raw(1))
+                        ->from('video_annotation_labels')
+                        ->whereRaw('video_annotation_labels.annotation_id = video_annotations.id')
+                        ->whereIn('video_annotation_labels.user_id', function ($query) {
+                            $query->select('user_id')
+                                ->from('annotation_session_user')
+                                ->where('annotation_session_id', $this->id);
+                        });
+                });
         });
     }
 }

app/Console/Commands/MigrateTiledImages.php

@@ -4,7 +4,6 @@
 
 use Biigle\Image;
 use Biigle\Jobs\MigrateTiledImage;
-use Biigle\Volume;
 use Illuminate\Console\Command;
 use Queue;
 

app/Console/Commands/UpdateVideoMetadata.php

@@ -65,7 +65,7 @@ public function processVolume(Volume $volume)
         $query = $volume->videos()
             ->where(function ($query) {
                 $query->whereNull('attrs->width')
-                ->orWhereNull('attrs->height');
+                    ->orWhereNull('attrs->height');
             });
 
         if ($volume->isRemote()) {

app/Console/Commands/UpdateVolumeUrls.php

@@ -65,9 +65,7 @@ protected function updateVolumes($volumes)
         $url = $volumes->first();
         $prefix = $this->ask('Please enter the volume URL prefix that you want to replace with a storage disk.', dirname($url));
 
-        $matches = $volumes->filter(function ($url) use ($prefix) {
-            return strpos($url, $prefix) === 0;
-        });
+        $matches = $volumes->filter(fn ($url) => strpos($url, $prefix) === 0);
         $matchesCount = $matches->count();
 
         if ($matchesCount > 0) {

app/Console/Kernel.php

@@ -27,7 +27,8 @@ protected function schedule(Schedule $schedule): void
             ->daily()
             ->onOneServer();
 
-        $schedule->call(function () {
+        $schedule
+            ->call(function () {
                 if (FederatedSearchInstance::withLocalToken()->exists()) {
                     GenerateFederatedSearchIndex::dispatch();
                 }
@@ -38,7 +39,8 @@ protected function schedule(Schedule $schedule): void
             ->hourlyAt(55)
             ->onOneServer();
 
-        $schedule->call(function () {
+        $schedule
+            ->call(function () {
                 FederatedSearchInstance::withRemoteToken()
                     ->eachById([UpdateFederatedSearchIndex::class, 'dispatch']);
             })

app/Events/ObjectTrackingFailed.php

@@ -5,10 +5,7 @@
 use Biigle\Broadcasting\UserChannel;
 use Biigle\User;
 use Biigle\VideoAnnotation;
-use Illuminate\Broadcasting\Channel;
 use Illuminate\Broadcasting\InteractsWithSockets;
-use Illuminate\Broadcasting\PresenceChannel;
-use Illuminate\Broadcasting\PrivateChannel;
 use Illuminate\Contracts\Broadcasting\ShouldBroadcastNow;
 use Illuminate\Foundation\Events\Dispatchable;
 use Illuminate\Queue\SerializesModels;

app/Events/ObjectTrackingSucceeded.php

@@ -5,10 +5,7 @@
 use Biigle\Broadcasting\UserChannel;
 use Biigle\User;
 use Biigle\VideoAnnotation;
-use Illuminate\Broadcasting\Channel;
 use Illuminate\Broadcasting\InteractsWithSockets;
-use Illuminate\Broadcasting\PresenceChannel;
-use Illuminate\Broadcasting\PrivateChannel;
 use Illuminate\Contracts\Broadcasting\ShouldBroadcastNow;
 use Illuminate\Foundation\Events\Dispatchable;
 use Illuminate\Queue\SerializesModels;

app/Http/Controllers/Api/AnnotationSessionController.php

@@ -2,7 +2,6 @@
 
 namespace Biigle\Http\Controllers\Api;
 
-use Biigle\AnnotationSession;
 use Biigle\Http\Requests\DestroyAnnotationSession;
 use Biigle\Http\Requests\UpdateAnnotationSession;
 use Biigle\Volume;

app/Http/Controllers/Api/Annotations/Filters/AnnotationUserController.php

@@ -54,12 +54,13 @@ public function index(Request $request, $tid, $uid)
         $ownerKeyName = $fileRelation->getQualifiedOwnerKeyName();
         $labelsRelation = $model->labels();
 
-        return $query->join($labelsRelation->getRelated()->getTable(), $labelsRelation->getQualifiedParentKeyName(), '=', $labelsRelation->getQualifiedForeignKeyName())
-                ->where($labelsRelation->getRelated()->user()->getQualifiedForeignKeyName(), $uid)
-                ->join($fileRelation->getRelated()->getTable(), $fileRelation->getQualifiedForeignKeyName(), '=', $ownerKeyName)
-                ->where($fileRelation->getRelated()->volume()->getQualifiedForeignKeyName(), $tid)
-                ->select($ownerKeyName)
-                ->distinct()
-                ->pluck($ownerKeyName);
+        return $query
+            ->join($labelsRelation->getRelated()->getTable(), $labelsRelation->getQualifiedParentKeyName(), '=', $labelsRelation->getQualifiedForeignKeyName())
+            ->where($labelsRelation->getRelated()->user()->getQualifiedForeignKeyName(), $uid)
+            ->join($fileRelation->getRelated()->getTable(), $fileRelation->getQualifiedForeignKeyName(), '=', $ownerKeyName)
+            ->where($fileRelation->getRelated()->volume()->getQualifiedForeignKeyName(), $tid)
+            ->select($ownerKeyName)
+            ->distinct()
+            ->pluck($ownerKeyName);
     }
 }

app/Http/Controllers/Api/AnnouncementController.php

@@ -2,9 +2,8 @@
 
 namespace Biigle\Http\Controllers\Api;
 
-use Biigle\Http\Requests\StoreAnnouncement;
 use Biigle\Announcement;
-use Illuminate\Http\Request;
+use Biigle\Http\Requests\StoreAnnouncement;
 
 class AnnouncementController extends Controller
 {

app/Http/Controllers/Api/ImageAnnotationBulkController.php

@@ -100,8 +100,8 @@ public function store(StoreImageAnnotations $request)
             $annotations->each(function ($annotation) use ($request) {
                 $label = $request->labels[$annotation->label_id];
                 $confidence = $annotation->confidence;
-                unset($annotation->label_id);
-                unset($annotation->confidence);
+                unset($annotation->label_id, $annotation->confidence);
+
                 $this->authorize('attach-label', [$annotation, $label]);
                 $annotation->save();
 

app/Http/Controllers/Api/ImageController.php

@@ -42,7 +42,6 @@ public function show($id)
         return $image;
     }
 
-
     /**
      * Shows the specified image file.
      *

app/Http/Controllers/Api/LabelTreeMergeController.php

@@ -2,7 +2,6 @@
 
 namespace Biigle\Http\Controllers\Api;
 
-use Biigle\Http\Controllers\Api\Controller;
 use Biigle\Http\Requests\StoreLabelTreeMerge;
 use Biigle\Label;
 use DB;

app/Http/Controllers/Api/LabelTreeVersionController.php

@@ -5,14 +5,12 @@
 use Biigle\Http\Requests\DestroyLabelTreeVersion;
 use Biigle\Http\Requests\StoreLabelTreeVersion;
 use Biigle\Http\Requests\UpdateLabelTreeVersion;
-use Biigle\LabelTree;
 use Biigle\LabelTreeVersion;
 use DB;
 use Ramsey\Uuid\Uuid;
 
 class LabelTreeVersionController extends Controller
 {
-
     /**
      * Creates a new label tree version.
      *

app/Http/Controllers/Api/LinkVideoAnnotationController.php

@@ -2,10 +2,8 @@
 
 namespace Biigle\Http\Controllers\Api;
 
-use Biigle\Http\Controllers\Api\Controller;
 use Biigle\Http\Requests\LinkVideoAnnotation;
 use Biigle\VideoAnnotation;
-use Biigle\VideoAnnotationLabel;
 use DB;
 
 class LinkVideoAnnotationController extends Controller

app/Http/Controllers/Api/ProjectController.php

@@ -6,7 +6,6 @@
 use Biigle\Http\Requests\UpdateProject;
 use Biigle\Project;
 use Illuminate\Http\Request;
-use Route;
 use Symfony\Component\HttpKernel\Exception\HttpException;
 
 class ProjectController extends Controller

app/Http/Controllers/Api/ProjectLabelTreeController.php

@@ -5,8 +5,6 @@
 use Biigle\Http\Requests\StoreProjectLabelTree;
 use Biigle\LabelTree;
 use Biigle\Project;
-use Biigle\Visibility;
-use Illuminate\Auth\Access\AuthorizationException;
 use Illuminate\Http\Request;
 
 class ProjectLabelTreeController extends Controller

app/Http/Controllers/Api/ProjectVolumeController.php

@@ -4,7 +4,6 @@
 
 use Biigle\Http\Requests\StoreVolume;
 use Biigle\Jobs\CreateNewImagesOrVideos;
-use Biigle\MediaType;
 use Biigle\Project;
 use Biigle\Volume;
 use DB;

app/Http/Controllers/Api/ProjectsAttachableVolumesController.php

@@ -2,7 +2,6 @@
 
 namespace Biigle\Http\Controllers\Api;
 
-use Biigle\Http\Controllers\Api\Controller;
 use Biigle\Project;
 use Biigle\Role;
 use Biigle\Volume;

app/Http/Controllers/Api/SplitVideoAnnotationController.php

@@ -2,7 +2,6 @@
 
 namespace Biigle\Http\Controllers\Api;
 
-use Biigle\Http\Controllers\Api\Controller;
 use Biigle\Http\Requests\SplitVideoAnnotation;
 use Biigle\Shape;
 use Biigle\VideoAnnotation;

app/Http/Controllers/Api/UserRegistrationController.php

@@ -8,7 +8,6 @@
 use Biigle\User;
 use Illuminate\Http\Request;
 use Illuminate\Http\Response;
-use Illuminate\Validation\ValidationException;
 
 class UserRegistrationController extends Controller
 {

app/Http/Controllers/Api/UserSettingsController.php

@@ -3,7 +3,6 @@
 namespace Biigle\Http\Controllers\Api;
 
 use Biigle\Http\Requests\UpdateUserSettings;
-use Illuminate\Http\Request;
 
 class UserSettingsController extends Controller
 {