Merge pull request #150 from biigle/merge-pgvector

Move feature vector models to default database connection
biigle · Dec 13, 2023 · 6d5bff4 · 6d5bff4
2 parents 95132b4 + 3eb56de
commit 6d5bff4
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Showing 13 changed files with 100 additions and 95 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -57,7 +57,7 @@ jobs:
         docker pull ghcr.io/biigle/worker:latest
 
     - name: Start test database
-      run: docker-compose up -d --no-build database_testing vector_database_testing && sleep 5
+      run: docker-compose up -d --no-build database_testing && sleep 5
       working-directory: ../core
 
     - name: Run tests

diff --git a/src/AnnotationCandidateFeatureVector.php b/src/AnnotationCandidateFeatureVector.php
@@ -12,13 +12,6 @@ class AnnotationCandidateFeatureVector extends Model
 {
     use HasFactory, HasNeighbors;
 
-    /**
-     * The database connection associated with the model.
-     *
-     * @var string
-     */
-    protected $connection = 'pgvector';
-
     /**
      * The table associated with the model.
      *

diff --git a/src/Database/Factories/AnnotationCandidateFeatureVectorFactory.php b/src/Database/Factories/AnnotationCandidateFeatureVectorFactory.php
@@ -3,6 +3,7 @@
 namespace Biigle\Modules\Maia\Database\Factories;
 
 use Biigle\Modules\Maia\MaiaJob;
+use Biigle\Modules\Maia\AnnotationCandidate;
 use Biigle\Modules\Maia\AnnotationCandidateFeatureVector;
 use Illuminate\Database\Eloquent\Factories\Factory;
 
@@ -23,7 +24,7 @@ class AnnotationCandidateFeatureVectorFactory extends Factory
     public function definition()
     {
         return [
-            'id' => $this->faker->unique()->randomDigit(),
+            'id' => AnnotationCandidate::factory(),
             'job_id' => MaiaJob::factory(),
             'vector' => range(0, 383),
         ];

diff --git a/src/Database/Factories/TrainingProposalFeatureVectorFactory.php b/src/Database/Factories/TrainingProposalFeatureVectorFactory.php
@@ -3,6 +3,7 @@
 namespace Biigle\Modules\Maia\Database\Factories;
 
 use Biigle\Modules\Maia\MaiaJob;
+use Biigle\Modules\Maia\TrainingProposal;
 use Biigle\Modules\Maia\TrainingProposalFeatureVector;
 use Illuminate\Database\Eloquent\Factories\Factory;
 
@@ -23,7 +24,7 @@ class TrainingProposalFeatureVectorFactory extends Factory
     public function definition()
     {
         return [
-            'id' => $this->faker->unique()->randomDigit(),
+            'id' => TrainingProposal::factory(),
             'job_id' => MaiaJob::factory(),
             'vector' => range(0, 383),
         ];

diff --git a/src/Database/migrations/2023_10_04_164500_create_feature_vectors_tables.php b/src/Database/migrations/2023_10_04_164500_create_feature_vectors_tables.php
@@ -13,27 +13,9 @@
      */
     public function up()
     {
-        Schema::connection('pgvector')
-            ->create('maia_training_proposal_feature_vectors', function (Blueprint $table) {
-                // Don't use increments() because it should throw an error if this is not
-                // manually provided. It should be the ID of the model in the main DB.
-                $table->unsignedInteger('id');
-                $table->unsignedInteger('job_id')->index();
-                $table->vector('vector', 384);
-
-                $table->primary('id');
-            });
-
-        Schema::connection('pgvector')
-            ->create('maia_annotation_candidate_feature_vectors', function (Blueprint $table) {
-                // Don't use increments() because it should throw an error if this is not
-                // manually provided. It should be the ID of the model in the main DB.
-                $table->unsignedInteger('id');
-                $table->unsignedInteger('job_id')->index();
-                $table->vector('vector', 384);
-
-                $table->primary('id');
-            });
+        // This migration set up tables in a separate pgvector database. The database was
+        // removed later. The migration was cleared so data in the separate database
+        // cannot be accidentally deleted.
     }
 
     /**
@@ -43,9 +25,6 @@ public function up()
      */
     public function down()
     {
-        Schema::connection('pgvector')
-            ->dropIfExists('maia_training_proposal_feature_vectors');
-        Schema::connection('pgvector')
-            ->dropIfExists('maia_annotation_candidate_feature_vectors');
+        //
     }
 };
diff --git a/src/Database/migrations/2023_12_12_150900_create_feature_vectors_tables.php b/src/Database/migrations/2023_12_12_150900_create_feature_vectors_tables.php
@@ -0,0 +1,59 @@
+<?php
+
+use Illuminate\Database\Migrations\Migration;
+use Illuminate\Database\Schema\Blueprint;
+use Illuminate\Support\Facades\Schema;
+
+return new class extends Migration
+{
+    /**
+     * Run the migrations.
+     *
+     * @return void
+     */
+    public function up()
+    {
+        Schema::create('maia_training_proposal_feature_vectors', function (Blueprint $table) {
+                $table->unsignedBigInteger('id');
+                $table->foreign('id')
+                    ->references('id')
+                    ->on('maia_training_proposals')
+                    ->onDelete('cascade');
+
+                $table->unsignedInteger('job_id')->index();
+                $table->foreign('job_id')
+                    ->references('id')
+                    ->on('maia_jobs')
+                    ->onDelete('cascade');
+
+                $table->vector('vector', 384);
+            });
+
+        Schema::create('maia_annotation_candidate_feature_vectors', function (Blueprint $table) {
+                $table->unsignedBigInteger('id');
+                $table->foreign('id')
+                    ->references('id')
+                    ->on('maia_annotation_candidates')
+                    ->onDelete('cascade');
+
+                $table->unsignedInteger('job_id')->index();
+                $table->foreign('job_id')
+                    ->references('id')
+                    ->on('maia_jobs')
+                    ->onDelete('cascade');
+
+                $table->vector('vector', 384);
+            });
+    }
+
+    /**
+     * Reverse the migrations.
+     *
+     * @return void
+     */
+    public function down()
+    {
+        Schema::dropIfExists('maia_training_proposal_feature_vectors');
+        Schema::dropIfExists('maia_annotation_candidate_feature_vectors');
+    }
+};
diff --git a/src/Listeners/DeleteAnnotationFeatureVectors.php b/src/Listeners/DeleteAnnotationFeatureVectors.php
diff --git a/src/MaiaServiceProvider.php b/src/MaiaServiceProvider.php
@@ -6,7 +6,6 @@
 use Biigle\Modules\Maia\Events\MaiaJobContinued;
 use Biigle\Modules\Maia\Events\MaiaJobCreated;
 use Biigle\Modules\Maia\Events\MaiaJobDeleting;
-use Biigle\Modules\Maia\Listeners\DeleteAnnotationFeatureVectors;
 use Biigle\Modules\Maia\Listeners\DispatchMaiaJob;
 use Biigle\Modules\Maia\Listeners\DispatchObjectDetection;
 use Biigle\Modules\Maia\Listeners\PrepareDeleteAnnotationPatches;
@@ -66,7 +65,6 @@ public function boot(Modules $modules, Router $router)
         Event::listen(MaiaJobContinued::class, PruneTrainingProposalPatches::class);
         Event::listen(MaiaJobContinued::class, PruneTrainingProposalFeatureVectors::class);
         Event::listen(MaiaJobDeleting::class, PrepareDeleteAnnotationPatches::class);
-        Event::listen(MaiaJobDeleting::class, DeleteAnnotationFeatureVectors::class);
     }
 
     /**

diff --git a/src/TrainingProposalFeatureVector.php b/src/TrainingProposalFeatureVector.php
@@ -12,13 +12,6 @@ class TrainingProposalFeatureVector extends Model
 {
     use HasFactory, HasNeighbors;
 
-    /**
-     * The database connection associated with the model.
-     *
-     * @var string
-     */
-    protected $connection = 'pgvector';
-
     /**
      * The table associated with the model.
      *

diff --git a/tests/AnnotationCandidateFeatureVectorTest.php b/tests/AnnotationCandidateFeatureVectorTest.php
@@ -2,6 +2,7 @@
 
 namespace Biigle\Tests\Modules\Maia;
 
+use Biigle\Modules\Maia\AnnotationCandidate;
 use Biigle\Modules\Maia\AnnotationCandidateFeatureVector;
 use Biigle\Shape;
 use TestCase;
@@ -14,4 +15,11 @@ public function testAttributes()
         $this->assertNotNull($model->job_id);
         $this->assertNotNull($model->vector);
     }
+
+    public function testCascadeDelete()
+    {
+        $model = AnnotationCandidateFeatureVector::factory()->create();
+        AnnotationCandidate::find($model->id)->delete();
+        $this->assertNull($model->fresh());
+    }
 }
diff --git a/tests/Listeners/DeleteAnnotationFeatureVectorsTest.php b/tests/Listeners/DeleteAnnotationFeatureVectorsTest.php
diff --git a/tests/MaiaJobTest.php b/tests/MaiaJobTest.php
@@ -2,6 +2,8 @@
 
 namespace Biigle\Tests\Modules\Maia;
 
+use Biigle\Modules\Maia\AnnotationCandidateFeatureVector;
+use Biigle\Modules\Maia\TrainingProposalFeatureVector;
 use Biigle\Modules\Maia\Events\MaiaJobCreated;
 use Biigle\Modules\Maia\Events\MaiaJobDeleting;
 use Biigle\Modules\Maia\MaiaJob;
@@ -144,4 +146,18 @@ public function testShouldShowTrainingProposals()
         ];
         $this->assertTrue($this->model->shouldShowTrainingProposals());
     }
+
+    public function testDeleteFeatureVectorsCascade()
+    {
+        $tp = TrainingProposalFeatureVector::factory()->create([
+            'job_id' => $this->model->id,
+        ]);
+        $ac = AnnotationCandidateFeatureVector::factory()->create([
+            'job_id' => $this->model->id,
+        ]);
+
+        $this->model->delete();
+        $this->assertNull($tp->fresh());
+        $this->assertNull($ac->fresh());
+    }
 }
diff --git a/tests/TrainingProposalFeatureVectorTest.php b/tests/TrainingProposalFeatureVectorTest.php
@@ -2,6 +2,7 @@
 
 namespace Biigle\Tests\Modules\Maia;
 
+use Biigle\Modules\Maia\TrainingProposal;
 use Biigle\Modules\Maia\TrainingProposalFeatureVector;
 use Biigle\Shape;
 use TestCase;
@@ -14,4 +15,11 @@ public function testAttributes()
         $this->assertNotNull($model->job_id);
         $this->assertNotNull($model->vector);
     }
+
+    public function testCascadeDelete()
+    {
+        $model = TrainingProposalFeatureVector::factory()->create();
+        TrainingProposal::find($model->id)->delete();
+        $this->assertNull($model->fresh());
+    }
 }