Merge branch 'master' into flat-label-list-tab

biigle · Jan 30, 2025 · 84f2fe7 · 84f2fe7
2 parents 47795de + fc7ad73
commit 84f2fe7
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Showing 12 changed files with 255 additions and 60 deletions.
diff --git a/src/Http/Requests/StoreLargoSession.php b/src/Http/Requests/StoreLargoSession.php
@@ -112,10 +112,18 @@ protected function getAffectedAnnotations($dismissed, $changed)
      */
     protected function imageAnotationsBelongToVolumes($annotations, $volumes)
     {
-        return !ImageAnnotation::join('images', 'image_annotations.image_id', '=', 'images.id')
-            ->whereIn('image_annotations.id', $annotations)
-            ->whereNotIn('images.volume_id', $volumes)
-            ->exists();
+        $chunkedAnnotations = array_chunk($annotations,config('biigle.db_param_limit') - count($volumes)); 
+        foreach($chunkedAnnotations as $chunkedAnnotation){
+            $queryReturn = ImageAnnotation::join('images', 'image_annotations.image_id', '=', 'images.id')
+                ->whereIn('image_annotations.id', $chunkedAnnotation)
+                ->whereNotIn('images.volume_id', $volumes)
+                ->exists();
+            if ($queryReturn){
+                return false;
+            }
+        }
+        return true;
+
     }
 
     /**
@@ -128,10 +136,17 @@ protected function imageAnotationsBelongToVolumes($annotations, $volumes)
      */
     protected function videoAnotationsBelongToVolumes($annotations, $volumes)
     {
-        return !VideoAnnotation::join('videos', 'video_annotations.video_id', '=', 'videos.id')
-            ->whereIn('video_annotations.id', $annotations)
-            ->whereNotIn('videos.volume_id', $volumes)
-            ->exists();
+        $chunkedAnnotations = array_chunk($annotations,config('biigle.db_param_limit') - count($volumes));
+        foreach($chunkedAnnotations as $chunkedAnnotation){
+            $queryReturn = VideoAnnotation::join('videos', 'video_annotations.video_id', '=', 'videos.id')
+                ->whereIn('video_annotations.id', $chunkedAnnotation)
+                ->whereNotIn('videos.volume_id', $volumes)
+                ->exists();
+            if ($queryReturn){
+                return false;
+            }
+        }
+        return true;
     }
 
     /**

diff --git a/src/Http/Requests/StoreProjectLargoSession.php b/src/Http/Requests/StoreProjectLargoSession.php
@@ -120,10 +120,17 @@ public function withValidator($validator)
      */
     protected function getAffectedImageVolumes($annotations)
     {
-        return ImageAnnotation::join('images', 'image_annotations.image_id', '=', 'images.id')
-            ->whereIn('image_annotations.id', $annotations)
-            ->distinct()
-            ->pluck('images.volume_id');
+        $chunkedAnnotations = array_chunk($annotations,config('biigle.db_param_limit'));
+        $volumeIdsArray = [];
+        foreach($chunkedAnnotations as $chunkedAnnotation){
+            $chunkVolumeId = ImageAnnotation::join('images', 'image_annotations.image_id', '=', 'images.id')
+                ->whereIn('image_annotations.id', $chunkedAnnotation)
+                ->distinct()
+                ->pluck('images.volume_id')
+                ->toArray();
+            $volumeIdsArray = array_merge($volumeIdsArray, $chunkVolumeId);
+        }
+        return array_unique($volumeIdsArray);
     }
 
     /**
@@ -136,9 +143,16 @@ protected function getAffectedImageVolumes($annotations)
      */
     protected function getAffectedVideoVolumes($annotations)
     {
-        return VideoAnnotation::join('videos', 'video_annotations.video_id', '=', 'videos.id')
-            ->whereIn('video_annotations.id', $annotations)
-            ->distinct()
-            ->pluck('videos.volume_id');
+        $chunkedAnnotations = array_chunk($annotations,config('biigle.db_param_limit'));
+        $volumeIdsArray = [];
+        foreach($chunkedAnnotations as $chunkedAnnotation){
+            $chunkVolumeId = VideoAnnotation::join('videos', 'video_annotations.video_id', '=', 'videos.id')
+                ->whereIn('video_annotations.id', $chunkedAnnotation)
+                ->distinct()
+                ->pluck('videos.volume_id')
+                ->toArray();
+            $volumeIdsArray = array_merge($volumeIdsArray, $chunkVolumeId);
+        }
+        return array_unique($volumeIdsArray);
     }
 }
diff --git a/src/Jobs/ApplyLargoSession.php b/src/Jobs/ApplyLargoSession.php
@@ -20,6 +20,7 @@
 use DB;
 use Illuminate\Contracts\Queue\ShouldQueue;
 use Illuminate\Queue\InteractsWithQueue;
+use Throwable;
 
 class ApplyLargoSession extends Job implements ShouldQueue
 {
@@ -120,23 +121,41 @@ public function __construct($id, User $user, $dismissedImageAnnotations, $change
      */
     public function handle()
     {
-        try {
-            DB::transaction(function () {
-                $this->handleImageAnnotations();
-                $this->handleVideoAnnotations();
-            });
-
-            LargoSessionSaved::dispatch($this->id, $this->user);
-        } catch (\Exception $e) {
-            LargoSessionFailed::dispatch($this->id, $this->user);
-        } finally {
-            Volume::where('attrs->largo_job_id', $this->id)->each(function ($volume) {
-                $attrs = $volume->attrs;
-                unset($attrs['largo_job_id']);
-                $volume->attrs = $attrs;
-                $volume->save();
-            });
+        if (!Volume::where('attrs->largo_job_id', $this->id)->exists()) {
+            // The job previously exited or failed. Don't run it twice.
+            // This can happen if the admin reruns failed jobs.
+            return;
         }
+
+        DB::transaction(function () {
+            $this->handleImageAnnotations();
+            $this->handleVideoAnnotations();
+        });
+
+        $this->cleanupJobId();
+        LargoSessionSaved::dispatch($this->id, $this->user);
+    }
+
+    /**
+     * Handle a job failure.
+     */
+    public function failed(?Throwable $exception): void
+    {
+        $this->cleanupJobId();
+        LargoSessionFailed::dispatch($this->id, $this->user);
+    }
+
+    /**
+     * Remove the properties that indicate that a save Largo session is in progress.
+     */
+    protected function cleanupJobId(): void
+    {
+        Volume::where('attrs->largo_job_id', $this->id)->each(function ($volume) {
+            $attrs = $volume->attrs;
+            unset($attrs['largo_job_id']);
+            $volume->attrs = $attrs;
+            $volume->save();
+        });
     }
 
     /**

diff --git a/src/public/assets/scripts/main.js b/src/public/assets/scripts/main.js
diff --git a/src/public/mix-manifest.json b/src/public/mix-manifest.json
@@ -1,4 +1,4 @@
 {
-    "/assets/scripts/main.js": "/assets/scripts/main.js?id=fb79978afc6a6d9745dd1e6ea7320e8f",
+    "/assets/scripts/main.js": "/assets/scripts/main.js?id=e1053b7af4d2947420a8f46c4fa630c8",
     "/assets/styles/main.css": "/assets/styles/main.css?id=0ef4b3ef391cbeaff5022f2ba61a6b05"
 }
diff --git a/src/resources/assets/js/components/settingsTab.vue b/src/resources/assets/js/components/settingsTab.vue
@@ -15,6 +15,7 @@
 <script>
 import Settings from '../stores/settings';
 import {PowerToggle} from '../import';
+import { Keyboard } from '../import';
 
 export default {
     components: {
@@ -51,6 +52,14 @@ export default {
         this.restoreKeys.forEach((key) => {
             this[key] = this.settings.get(key);
         });
+
+        Keyboard.on('o', () => {
+            if (this.showOutlines) {
+                this.disableOutlines();
+            } else {
+                this.enableOutlines();
+            }
+        });
     },
 };
 </script>

diff --git a/src/resources/assets/js/import.js b/src/resources/assets/js/import.js
@@ -12,3 +12,4 @@ export let Settings = biigle.$require('core.models.Settings');
 export let SettingsTabPlugins = biigle.$require('annotations.components.settingsTabPlugins');
 export let Sidebar = biigle.$require('core.components.sidebar');
 export let SidebarTab = biigle.$require('core.components.sidebarTab');
+export let Keyboard = biigle.$require('core.keyboard');
diff --git a/src/resources/assets/js/mixins/largoContainer.vue b/src/resources/assets/js/mixins/largoContainer.vue
@@ -89,8 +89,7 @@ export default {
                 return annotations;
             }
 
-            // This will be empty for the default sorting.
-            if (this.sortingSequence.length > 0) {
+            if (this.sortingKey !== SORT_KEY.ANNOTATION_ID) {
                 const map = {};
                 annotations.forEach((a) => {
                     // Image annotation IDs are prefixed with 'i', video annotations with

diff --git a/src/resources/views/manual/tutorials/largo.blade.php b/src/resources/views/manual/tutorials/largo.blade.php
@@ -140,7 +140,7 @@
 
         <dl>
             <dt>Show annotation outlines</dt>
-            <dd>Disable this option to hide the outlines of the annotation on each patch (enabled by default).</dd>
+            <dd>Disable this option to hide the outlines of the annotation on each patch (enabled by default). Use the <kbd>o</kbd> key as shortcut.</dd>
         </dl>
 
         <h3><a name="example-use-cases"></a>Example use cases</h3>

diff --git a/tests/Http/Controllers/Api/Projects/LargoControllerTest.php b/tests/Http/Controllers/Api/Projects/LargoControllerTest.php
@@ -4,6 +4,9 @@
 
 use ApiTestCase;
 use Biigle\MediaType;
+use Biigle\ImageAnnotation;
+use Biigle\VideoAnnotation;
+use Biigle\Label;
 use Biigle\Modules\Largo\Jobs\ApplyLargoSession;
 use Biigle\Modules\Largo\Jobs\RemoveImageAnnotationPatches;
 use Biigle\Modules\Largo\Jobs\RemoveVideoAnnotationPatches;
@@ -443,4 +446,62 @@ public function testStoreJobStillRunningVideoAnnotations()
                 'changed_video_annotations' => [],
             ])->assertStatus(422);
     }
+
+    public function testChunkingImgProject()
+    {
+        config(['biigle.db_param_limit' => 2]);
+        $image = ImageTest::create(['volume_id' => $this->imageVolume->id,
+                                    'filename' => "testImage"]);
+
+        $imageAnnotations = ImageAnnotation::factory()->count(5)->create(['image_id' => $image->id]);
+        $label = Label::factory()->create(); 
+
+
+        $imageAnnotations->each(fn($imageAnnotation) =>
+            ImageAnnotationLabelTest::create([
+                'annotation_id' => $imageAnnotation->id,
+                'user_id' => $this->editor()->id,
+                'label_id' => $label->id,
+            ]));
+
+
+        $this->beEditor();
+        $this->postJson("/api/v1/projects/{$this->project()->id}/largo", [
+                'dismissed_image_annotations' => [
+                    $this->imageAnnotationLabel->label_id => $imageAnnotations->pluck('id'), 
+                ],
+                'changed_image_annotations' => [],
+            ])
+            ->assertStatus(200);
+        Queue::assertPushed(ApplyLargoSession::class);
+    }
+
+    public function testChunkingVidProject()
+    {
+        config(['biigle.db_param_limit' => 2]);
+        $video = VideoTest::create(['volume_id' => $this->videoVolume->id,
+                                    'filename' => "testVideo"]);
+        $videoAnnotations = VideoAnnotation::factory()->count(5)->create(['video_id' => $video->id]);
+
+        $label = Label::factory()->create(); 
+
+        $videoAnnotations->each(fn($videoAnnotation) =>
+            VideoAnnotationLabelTest::create([
+                'annotation_id' => $videoAnnotation->id,
+                'user_id' => $this->editor()->id,
+                'label_id' => $label->id,
+            ]));
+
+
+        $this->beEditor();
+        $this->postJson("/api/v1/projects/{$this->project()->id}/largo", [
+                'dismissed_video_annotations' => [
+                    $this->videoAnnotationLabel->label_id => $videoAnnotations->pluck('id'), 
+                ],
+                'changed_video_annotations' => [],
+            ])
+            ->assertStatus(200);
+        Queue::assertPushed(ApplyLargoSession::class);
+    }
+
 }
diff --git a/tests/Http/Controllers/Api/Volumes/LargoControllerTest.php b/tests/Http/Controllers/Api/Volumes/LargoControllerTest.php
@@ -4,6 +4,9 @@
 
 use ApiTestCase;
 use Biigle\MediaType;
+use Biigle\ImageAnnotation;
+use Biigle\VideoAnnotation;
+use Biigle\Label;
 use Biigle\Modules\Largo\Jobs\ApplyLargoSession;
 use Biigle\Modules\Largo\Jobs\RemoveImageAnnotationPatches;
 use Biigle\Modules\Largo\Jobs\RemoveVideoAnnotationPatches;
@@ -439,4 +442,63 @@ public function testStoreJobStillRunningVideoAnnotations()
                 'changed_video_annotations' => [],
             ])->assertStatus(422);
     }
+
+
+    public function testChunkingImgVol()
+    {
+        config(['biigle.db_param_limit' => 2]);
+        $image = ImageTest::create(['volume_id' => $this->imageVolume->id,
+                                    'filename' => "testImage"]);
+
+        $imageAnnotations = ImageAnnotation::factory()->count(5)->create(['image_id' => $image->id]);
+        $label = Label::factory()->create(); 
+
+
+        $imageAnnotations->each(fn($imageAnnotation) =>
+            ImageAnnotationLabelTest::create([
+                'annotation_id' => $imageAnnotation->id,
+                'user_id' => $this->editor()->id,
+                'label_id' => $label->id,
+            ]));
+
+
+        $this->beEditor();
+        $this->postJson("/api/v1/volumes/{$this->imageVolume->id}/largo", [
+                'dismissed_image_annotations' => [
+                    $this->imageAnnotationLabel->label_id => $imageAnnotations->pluck('id'), 
+                ],
+                'changed_image_annotations' => [],
+            ])
+            ->assertStatus(200);
+        Queue::assertPushed(ApplyLargoSession::class);
+    }
+
+    public function testChunkingVidVol()
+    {
+        config(['biigle.db_param_limit' => 2]);
+        $video = VideoTest::create(['volume_id' => $this->videoVolume->id,
+                                    'filename' => "testVideo"]);
+        $videoAnnotations = VideoAnnotation::factory()->count(5)->create(['video_id' => $video->id]);
+
+        $label = Label::factory()->create(); 
+
+        $videoAnnotations->each(function($videoAnnotation) use($label){
+            VideoAnnotationLabelTest::create([
+                'annotation_id' => $videoAnnotation->id,
+                'user_id' => $this->editor()->id,
+                'label_id' => $label->id,
+            ]);
+        });
+
+
+        $this->beEditor();
+        $this->postJson("/api/v1/volumes/{$this->videoVolume->id}/largo", [
+                'dismissed_video_annotations' => [
+                    $this->videoAnnotationLabel->label_id => $videoAnnotations->pluck('id'), 
+                ],
+                'changed_video_annotations' => [],
+            ])
+            ->assertStatus(200);
+        Queue::assertPushed(ApplyLargoSession::class);
+    }
 }