Implement project largo sort by outlier controller

biigle · Jan 11, 2024 · a5b75b4 · a5b75b4
1 parent 6960687
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Showing 5 changed files with 177 additions and 4 deletions.
diff --git a/src/Http/Controllers/Api/Projects/SortAnnotationsByOutliersController.php b/src/Http/Controllers/Api/Projects/SortAnnotationsByOutliersController.php
@@ -0,0 +1,74 @@
+<?php
+
+namespace Biigle\Modules\Largo\Http\Controllers\Api\Projects;
+
+use DB;
+use Biigle\Http\Controllers\Api\Controller;
+use Biigle\Modules\Largo\ImageAnnotationLabelFeatureVector;
+use Biigle\Modules\Largo\VideoAnnotationLabelFeatureVector;
+use Biigle\Project;
+
+class SortAnnotationsByOutliersController extends Controller
+{
+    /**
+     * Sort annotations with specific label by outliers.
+     *
+     * @api {get} projects/:pid/annotations/sort/outliers/:lid Sort annotations with the same label by outliers
+     * @apiGroup Projects
+     * @apiName ShowProjectsAnnotationsSortOutliers
+     * @apiParam {Number} pid The project ID
+     * @apiParam {Number} lid The Label ID
+     * @apiPermission projectMember
+     * @apiDescription Returns a list of image/video annotation IDs with the outliers first.
+     *
+     * @param  int  $pid Project ID
+     * @param int $lid Label ID
+     * @return \Illuminate\Http\Response
+     */
+    public function index($pid, $lid)
+    {
+        $project = Project::findOrFail($pid);
+        $this->authorize('access', $project);
+
+        // This was too complicated with the query builder. Since there is no rist of SQL
+        // injection here, we just use raw SQL.
+        $sql = <<<SQL
+        SELECT "id" FROM (
+            (
+              SELECT CONCAT('i', "annotation_id") AS id, "vector"
+              FROM "image_annotation_label_feature_vectors"
+              WHERE "label_id" = :lid AND "volume_id" IN (
+                 SELECT "volume_id" FROM "project_volume" WHERE "project_id" = :pid
+              )
+           )
+           UNION
+           (
+              SELECT CONCAT('v', "annotation_id") AS id, "vector"
+              FROM "video_annotation_label_feature_vectors"
+              WHERE "label_id" = :lid AND "volume_id" IN (
+                 SELECT "volume_id" FROM "project_volume" WHERE "project_id" = :pid
+              )
+           )
+        ) AS "temp"
+        ORDER BY "temp"."vector" <=> (
+            SELECT AVG("temp2"."vector") FROM (
+              SELECT "vector" FROM "image_annotation_label_feature_vectors"
+              WHERE "label_id" = :lid AND "volume_id" IN (
+                 SELECT "volume_id" FROM "project_volume" WHERE "project_id" = :pid
+              )
+              UNION ALL
+              SELECT "vector" FROM "video_annotation_label_feature_vectors"
+              WHERE "label_id" = :lid AND "volume_id" IN (
+                 SELECT "volume_id" FROM "project_volume" WHERE "project_id" = :pid
+              )
+           ) AS temp2
+        ) DESC, id DESC
+        SQL;
+
+        $ids = DB::select($sql, ['pid' => $pid, 'lid' => $lid]);
+
+        // Filtering unique IDs is not required here because the UNIQUE in the query
+        // takes care of that.
+        return array_map(fn ($v) => $v->id, $ids);
+    }
+}
diff --git a/src/Http/Controllers/Api/Volumes/SortAnnotationsByOutliersController.php b/src/Http/Controllers/Api/Volumes/SortAnnotationsByOutliersController.php
@@ -32,11 +32,11 @@ public function index($vid, $lid)
         if ($volume->isVideoVolume()) {
             $query = VideoAnnotationLabelFeatureVector::where('volume_id', $vid)
                 ->where('label_id', $lid)
-                ->orderByRaw('vector <=> (SELECT avg(vector) FROM video_annotation_label_feature_vectors WHERE volume_id = ? AND label_id = ?) DESC, annotation_id DESC', [$vid, $lid]);
+                ->orderByRaw('vector <=> (SELECT AVG(vector) FROM video_annotation_label_feature_vectors WHERE volume_id = ? AND label_id = ?) DESC, annotation_id DESC', [$vid, $lid]);
         } else {
             $query = ImageAnnotationLabelFeatureVector::where('volume_id', $vid)
                 ->where('label_id', $lid)
-                ->orderByRaw('vector <=> (SELECT avg(vector) FROM image_annotation_label_feature_vectors WHERE volume_id = ? AND label_id = ?) DESC, annotation_id DESC', [$vid, $lid]);
+                ->orderByRaw('vector <=> (SELECT AVG(vector) FROM image_annotation_label_feature_vectors WHERE volume_id = ? AND label_id = ?) DESC, annotation_id DESC', [$vid, $lid]);
         }
 
         return $query->pluck('annotation_id')

diff --git a/src/Http/routes.php b/src/Http/routes.php
@@ -33,6 +33,10 @@
         'uses' => 'Labels\VideoAnnotationsController@index',
     ]);
 
+    $router->get('projects/{id}/annotations/sort/outliers/{id2}', [
+        'uses' => 'Projects\SortAnnotationsByOutliersController@index',
+    ]);
+
     $router->get('projects/{id}/image-annotations/filter/label/{id2}', [
         'uses' => 'Projects\FilterImageAnnotationsByLabelController@index',
     ]);

diff --git a/tests/Http/Controllers/Api/Projects/SortAnnotationsByOutliersControllerTest.php b/tests/Http/Controllers/Api/Projects/SortAnnotationsByOutliersControllerTest.php
@@ -0,0 +1,95 @@
+<?php
+
+namespace Biigle\Tests\Modules\Largo\Http\Controllers\Api\Projects;
+
+use ApiTestCase;
+use Biigle\MediaType;
+use Biigle\Volume;
+use Biigle\Modules\Largo\ImageAnnotationLabelFeatureVector;
+use Biigle\Modules\Largo\VideoAnnotationLabelFeatureVector;
+
+class SortAnnotationsByOutliersControllerTest extends ApiTestCase
+{
+    public function testIndex()
+    {
+        $id = $this->project()->id;
+
+        $v1 = Volume::factory()->create();
+        $this->project()->addVolumeId($v1->id);
+
+        $l1 = ImageAnnotationLabelFeatureVector::factory()->create([
+            'volume_id' => $v1->id,
+        ]);
+        $l2 = ImageAnnotationLabelFeatureVector::factory()->create([
+            'volume_id' => $v1->id,
+            'label_id' => $l1->label_id,
+        ]);
+        $l3 = ImageAnnotationLabelFeatureVector::factory()->create([
+            'volume_id' => $v1->id,
+            'label_id' => $l1->label_id,
+            // The other feature vectors are identical so this one will be an outlier.
+            'vector' => range(1, 384),
+        ]);
+        $l4 = ImageAnnotationLabelFeatureVector::factory()->create([
+            'volume_id' => $v1->id,
+        ]);
+
+        $v2 = Volume::factory()->create(['media_type_id' => MediaType::videoId()]);
+        $this->project()->addVolumeId($v2->id);
+
+        $l5 = VideoAnnotationLabelFeatureVector::factory()->create([
+            'volume_id' => $v2->id,
+            'label_id' => $l1->label_id,
+        ]);
+        $l6 = VideoAnnotationLabelFeatureVector::factory()->create([
+            'volume_id' => $v2->id,
+            'label_id' => $l1->label_id,
+            'vector' => range(1, 384),
+        ]);
+
+        // Annotations from other volume should not appear.
+        ImageAnnotationLabelFeatureVector::factory()->create();
+        VideoAnnotationLabelFeatureVector::factory()->create();
+
+        $this->doTestApiRoute('GET', "/api/v1/projects/{$id}/annotations/sort/outliers/{$l1->label_id}");
+
+        $this->beUser();
+        $this->get("/api/v1/projects/{$id}/annotations/sort/outliers/{$l1->label_id}")
+            ->assertStatus(403);
+
+        $this->beGuest();
+
+        $this->get("/api/v1/projects/{$id}/annotations/sort/outliers/{$l1->label_id}")
+            ->assertStatus(200)
+            ->assertExactJson([
+                'v'.$l6->annotation_id,
+                'i'.$l3->annotation_id,
+                'v'.$l5->annotation_id,
+                'i'.$l2->annotation_id,
+                'i'.$l1->annotation_id,
+            ]);
+
+        $this->get("/api/v1/projects/{$id}/annotations/sort/outliers/{$l4->label_id}")
+            ->assertStatus(200)
+            ->assertExactJson(['i'.$l4->annotation_id]);
+    }
+
+    public function testIndexDuplicate()
+    {
+        $id = $this->project()->id;
+        $vid = $this->volume()->id;
+        $l1 = ImageAnnotationLabelFeatureVector::factory()->create([
+            'volume_id' => $vid,
+        ]);
+        $l2 = ImageAnnotationLabelFeatureVector::factory()->create([
+            'volume_id' => $vid,
+            'label_id' => $l1->label_id,
+            'annotation_id' => $l1->annotation_id,
+        ]);
+
+        $this->beEditor();
+        $this->get("/api/v1/projects/{$id}/annotations/sort/outliers/{$l1->label_id}")
+            ->assertStatus(200)
+            ->assertExactJson(['i'.$l1->annotation_id]);
+    }
+}
diff --git a/tests/Http/Controllers/Api/Volumes/SortAnnotationsByOutliersControllerTest.php b/tests/Http/Controllers/Api/Volumes/SortAnnotationsByOutliersControllerTest.php
@@ -44,8 +44,8 @@ public function testIndexImage()
             ->assertStatus(200)
             ->assertExactJson([
                 $l3->annotation_id,
-                $l1->annotation_id,
                 $l2->annotation_id,
+                $l1->annotation_id,
             ]);
 
         $this->get("/api/v1/volumes/{$id}/annotations/sort/outliers/{$l4->label_id}")
@@ -106,8 +106,8 @@ public function testIndexVideo()
             ->assertStatus(200)
             ->assertExactJson([
                 $l3->annotation_id,
-                $l1->annotation_id,
                 $l2->annotation_id,
+                $l1->annotation_id,
             ]);
 
         $this->get("/api/v1/volumes/{$id}/annotations/sort/outliers/{$l4->label_id}")