biigle · mzur · Oct 11, 2023 · Sep 15, 2023 · Sep 15, 2023 · Sep 15, 2023
diff --git a/.gitignore b/.gitignore
@@ -18,6 +18,5 @@ npm-debug.log
 yarn-error.log
 /*.sublime-*
 /*.phar
-/*.php_cs.cache
+/*.php-cs-fixer.cache
 /.idea
-/.vscode
diff --git a/.php-cs-fixer.php b/.php-cs-fixer.php
@@ -11,8 +11,7 @@
     ->setRules([
         '@PSR2' => true,
         'ordered_imports' => true,
-        'single_space_after_construct' => true,
-        'single_quote' => true,
+        'single_space_around_construct' => true,
         'array_indentation' => true,
         'array_syntax' => ['syntax' => 'short'],
         'combine_consecutive_unsets' => true,
@@ -21,10 +20,9 @@
         'unary_operator_spaces' => true,
         'whitespace_after_comma_in_array' => true,
         'method_chaining_indentation' => true,
-        'heredoc_indentation' => [
-            'indentation' => 'start_plus_one',
-        ],
-
+        'use_arrow_functions' => true,
+        'no_unused_imports' => true
     ])
     ->setFinder($finder)
+    ->setRiskyAllowed(true)
     ->setUsingCache(true);
diff --git a/CONTRIBUTING.md b/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.
diff --git a/app/Annotation.php b/app/Annotation.php
@@ -60,7 +60,8 @@ public function scopeVisibleFor($query, User $user)
                 ->join($ownerTable, $ownerKeyName, '=', $foreignKeyName)
                 ->join('project_volume', 'project_volume.volume_id', '=', "{$ownerTable}.volume_id")
                 ->whereIn('project_volume.project_id', function ($query) use ($user) {
-                    $query->select('project_id')
+                    $query
+                        ->select('project_id')
                         ->from('project_user')
                         ->where('user_id', $user->id);
                 });
@@ -109,8 +110,9 @@ public function scopeAllowedBySession($query, AnnotationSession $session, User $
                     $foreignKeyName = $this->labels()->getQualifiedForeignKeyName();
                     $foreignTable = explode('.', $foreignKeyName)[0];
                     $parentKeyName = $this->labels()->getQualifiedParentKeyName();
-
-                    $query->select(DB::raw(1))
+
+                    $query
+                        ->select(DB::raw(1))
                         ->from($foreignTable)
                         ->whereRaw("{$foreignKeyName} = {$parentKeyName}")
                         ->where("{$foreignTable}.user_id", $user->id);
@@ -126,7 +128,8 @@ public function scopeAllowedBySession($query, AnnotationSession $session, User $
                         $foreignTable = explode('.', $foreignKeyName)[0];
                         $parentKeyName = $this->labels()->getQualifiedParentKeyName();
 
-                        $query->select(DB::raw(1))
+                        $query
+                            ->select(DB::raw(1))
                             ->from($foreignTable)
                             ->whereRaw("{$foreignKeyName} = {$parentKeyName}")
                             ->where("{$foreignTable}.user_id", '!=', $user->id);
@@ -140,7 +143,8 @@ public function scopeAllowedBySession($query, AnnotationSession $session, User $
                 $foreignTable = explode('.', $foreignKeyName)[0];
                 $parentKeyName = $this->labels()->getQualifiedParentKeyName();
 
-                $query->select(DB::raw(1))
+                $query
+                    ->select(DB::raw(1))
                     ->from($foreignTable)
                     ->whereRaw("{$foreignKeyName} = {$parentKeyName}")
                     ->where("{$foreignTable}.user_id", $user->id);

diff --git a/app/AnnotationSession.php b/app/AnnotationSession.php
@@ -94,10 +94,11 @@ public function getVolumeFileAnnotations(VolumeFile $file, User $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)
+                        $query
+                            ->where('created_at', '>=', $this->starts_at)
                             ->where('created_at', '<', $this->ends_at);
                     })
-                    ->orWhere('user_id', '!=', $user->id);
+                        ->orWhere('user_id', '!=', $user->id);
                 });
             }]);
         } else {
@@ -206,24 +207,27 @@ public function imageAnnotations()
         return ImageAnnotation::where(function ($query) {
             // all annotations of the associated volume
             return $query->whereIn('image_id', function ($query) {
-                $query->select('id')
-                        ->from('images')
-                        ->where('volume_id', $this->volume_id);
+                $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)
+                ->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', $this->id);
-                    });
-            });
+                ->whereExists(function ($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);
+                        });
+                });
         });
     }
 
@@ -239,24 +243,27 @@ public function videoAnnotations()
         return VideoAnnotation::where(function ($query) {
             // all annotations of the associated volume
             return $query->whereIn('video_id', function ($query) {
-                $query->select('id')
-                        ->from('videos')
-                        ->where('volume_id', $this->volume_id);
+                $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)
+                ->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', $this->id);
-                    });
-            });
+                ->whereExists(function ($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', $this->id);
+                        });
+                });
         });
     }
 }
diff --git a/app/Announcement.php b/app/Announcement.php
@@ -74,7 +74,8 @@ public static function getActive()
     public function scopeActive($query)
     {
         return $query->where(function ($query) {
-            $query->whereNull('show_until')
+            $query
+                ->whereNull('show_until')
                 ->orWhere('show_until', '>', now());
         });
     }

diff --git a/app/Console/Commands/MigrateTiledImages.php b/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;
 

diff --git a/app/Console/Commands/UpdateVideoMetadata.php b/app/Console/Commands/UpdateVideoMetadata.php
@@ -62,10 +62,12 @@ public function handle()
 
     public function processVolume(Volume $volume)
     {
-        $query = $volume->videos()
+        $query = $volume
+            ->videos()
             ->where(function ($query) {
-                $query->whereNull('attrs->width')
-                ->orWhereNull('attrs->height');
+                $query
+                    ->whereNull('attrs->width')
+                    ->orWhereNull('attrs->height');
             });
 
         if ($volume->isRemote()) {
@@ -93,7 +95,8 @@ public function processRemoteVideo(Video $video)
         $this->line('Processing '.$video->url);
 
         try {
-            $dimensions = $this->ffprobe->streams($video->url)
+            $dimensions = $this->ffprobe
+                ->streams($video->url)
                 ->videos()
                 ->first()
                 ->getDimensions();

diff --git a/app/Console/Commands/UpdateVolumeUrls.php b/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) {

diff --git a/app/Console/Kernel.php b/app/Console/Kernel.php
@@ -18,29 +18,31 @@ class Kernel extends ConsoleKernel
      */
     protected function schedule(Schedule $schedule)
     {
-        $schedule->command('queue:prune-batches')
+        $schedule
+            ->command('queue:prune-batches')
             ->daily()
             ->onOneServer();
 
-        $schedule->command('prune-notifications')
+        $schedule
+            ->command('prune-notifications')
             ->daily()
             ->onOneServer();
 
         $schedule->call(function () {
-                if (FederatedSearchInstance::withLocalToken()->exists()) {
-                    GenerateFederatedSearchIndex::dispatch();
-                }
-            })
+            if (FederatedSearchInstance::withLocalToken()->exists()) {
+                GenerateFederatedSearchIndex::dispatch();
+            }
+        })
             ->name('generate-federated-search-index')
             // The requests to retrieve the federated search index are sent hourly at 05.
             // This should not collide with this job to generate the index.
             ->hourlyAt(55)
             ->onOneServer();
 
         $schedule->call(function () {
-                FederatedSearchInstance::withRemoteToken()
-                    ->eachById([UpdateFederatedSearchIndex::class, 'dispatch']);
-            })
+            FederatedSearchInstance::withRemoteToken()
+                ->eachById([UpdateFederatedSearchIndex::class, 'dispatch']);
+        })
             ->name('update-federated-search-index')
             // The jobs to generate the federated search index are run hourly at 55.
             // This should not collide with this job to request the index from another

diff --git a/app/Events/ObjectTrackingFailed.php b/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;

diff --git a/app/Events/ObjectTrackingSucceeded.php b/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;

diff --git a/app/Http/Controllers/Api/AnnotationSessionController.php b/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;
@@ -50,7 +49,8 @@ public function update(UpdateAnnotationSession $request)
         $session = $request->session;
 
         if ($request->filled('starts_at')) {
-            $newStartsAt = Carbon::parse($request->input('starts_at'))
+            $newStartsAt = Carbon::parse($request
+                ->input('starts_at'))
                 ->tz(config('app.timezone'));
 
             if (!$request->input('force') && $session->annotations()->where('created_at', '<', $newStartsAt)->exists()) {
@@ -61,7 +61,8 @@ public function update(UpdateAnnotationSession $request)
         }
 
         if ($request->filled('ends_at')) {
-            $newEndsAt = Carbon::parse($request->input('ends_at'))
+            $newEndsAt = Carbon::parse($request
+                ->input('ends_at'))
                 ->tz(config('app.timezone'));
 
             if (!$request->input('force') && $session->annotations()->where('created_at', '>=', $newEndsAt)->exists()) {
@@ -94,15 +95,18 @@ public function update(UpdateAnnotationSession $request)
                 if ($lostUsers->count() > 0) {
                     // Check if there are any annotations of the users that should no
                     // longer belong to the annotation session.
-                    $wouldLooseAnnotations = $session->annotations()
+                    $wouldLooseAnnotations = $session
+                        ->annotations()
                         ->whereExists(function ($query) use ($session, $lostUsers) {
                             // This must work with image annotations and video
                             // annotations.
-                            $labelModel = $session->annotations()
+                            $labelModel = $session
+                                ->annotations()
                                 ->getModel()
                                 ->labels()
                                 ->getRelated();
-                            $query->select(DB::raw(1))
+                            $query
+                                ->select(DB::raw(1))
                                 ->from($labelModel->getTable())
                                 ->whereRaw($labelModel->annotation()->getQualifiedForeignKeyName().' = '.$labelModel->annotation()->getQualifiedOwnerKeyName())
                                 ->whereIn($labelModel->user()->getQualifiedForeignKeyName(), $lostUsers);
@@ -116,7 +120,8 @@ public function update(UpdateAnnotationSession $request)
             }
 
             // count users of all attached projects that match the given user IDs
-            $count = $session->volume->users()
+            $count = $session->volume
+                ->users()
                 ->whereIn('id', $users)
                 ->count();
 

diff --git a/app/Http/Controllers/Api/Annotations/Filters/AnnotationUserController.php b/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($ownerKeyName);
     }
 }
diff --git a/app/Http/Controllers/Api/Annotations/VolumeAnnotationLabelController.php b/app/Http/Controllers/Api/Annotations/VolumeAnnotationLabelController.php
@@ -58,7 +58,8 @@ public function index($id)
                 $labelsRelation = $model->labels();
                 $labelsForeignKey = $labelsRelation->getRelated()->label()->getQualifiedForeignKeyName();
                 // take only labels that are used in annotations of this volume
-                $query->select(DB::raw(1))
+                $query
+                    ->select(DB::raw(1))
                     ->from($fileRelation->getRelated()->getTable())
                     ->join($model->getTable(), $fileRelation->getQualifiedOwnerKeyName(), '=', $fileRelation->getQualifiedForeignKeyName())
                     ->join($labelsRelation->getRelated()->getTable(), $labelsRelation->getQualifiedParentKeyName(), '=', $labelsRelation->getQualifiedForeignKeyName())