Merge branch 'master' into create-volume-v2

Author: mzur

.env.example

@@ -21,12 +21,6 @@ DB_DATABASE="biigle"
 DB_USERNAME="biigle"
 DB_PASSWORD="secret"
 
-VECTOR_DB_HOST="vector_database"
-VECTOR_DB_PORT=5432
-VECTOR_DB_DATABASE="biigle"
-VECTOR_DB_USERNAME="biigle"
-VECTOR_DB_PASSWORD="secret"
-
 VOLUME_ADMIN_STORAGE_DISKS=local
 
 BROADCAST_DRIVER=pusher

.github/workflows/test.yml

@@ -37,7 +37,6 @@ jobs:
     - name: Start test database
       run: |
         docker-compose up -d --no-build database_testing
-        docker-compose up -d --no-build vector_database_testing
         sleep 5
 
     - name: Run tests
@@ -80,7 +79,6 @@ jobs:
     - name: Start test database
       run: |
         docker-compose up -d --no-build database_testing
-        docker-compose up -d --no-build vector_database_testing
         sleep 5
 
     - name: Run tests

DEVELOPING.md

@@ -34,7 +34,7 @@ composer create-project biigle/core:dev-dev-modules \
 
 Note the `--ignore-platform-reqs` flag to keep Composer from complaining about missing requirements. These requirements will be met by the Docker containers.
 
-This will set up the project in the `dev-modules` branch of this repository. The `dev-modules` branch is configured with all BIIGLE modules which makes it easy to start module development. If you want to develop a feature directly in `biigle/core`, please switch to the `master` branch (or create your own branch based on `master`).
+This will set up the project in the `dev-modules` branch of this repository. The `dev-modules` branch is configured with all BIIGLE modules which makes it easy to start module development. If you want to develop a feature directly in `biigle/core`, please switch to the `master` branch (or create your own branch based on `master`). Pull requests from a `dev-modules`-based branch will not be accepted.
 
 ### 2. Build and run the application
 

config/database.php

@@ -78,21 +78,6 @@
             'sslmode' => 'prefer',
         ],
 
-        'pgvector' => [
-            'driver' => 'pgsql',
-            'url' => env('VECTOR_DATABASE_URL'),
-            'host' => env('VECTOR_DB_HOST', 'localhost'),
-            'port' => env('VECTOR_DB_PORT', '5432'),
-            'database' => env('VECTOR_DB_DATABASE', 'forge'),
-            'username' => env('VECTOR_DB_USERNAME', 'forge'),
-            'password' => env('VECTOR_DB_PASSWORD', ''),
-            'charset' => 'utf8',
-            'prefix' => '',
-            'prefix_indexes' => true,
-            'search_path' => 'public',
-            'sslmode' => 'prefer',
-        ],
-
         'sqlsrv' => [
             'driver' => 'sqlsrv',
             'url' => env('DATABASE_URL'),

database/migrations/2022_08_03_000000_create_vector_extension.php

@@ -11,7 +11,14 @@
      */
     public function up()
     {
-        DB::connection('pgvector')->statement('CREATE EXTENSION IF NOT EXISTS vector');
+        // The pgvector connection was removed later so it may not always be present.
+        // There is a second migration that enables pgvector for the default connection.
+        // See: https://github.com/biigle/maia/pull/150
+        if (!is_null(config('database.connections-pgvector'))) {
+            DB::connection('pgvector')
+                ->statement('CREATE EXTENSION IF NOT EXISTS vector');
+
+        }
     }
 
     /**
@@ -21,6 +28,10 @@ public function up()
      */
     public function down()
     {
-        DB::connection('pgvector')->statement('DROP EXTENSION IF EXISTS vector');
+        if (!is_null(config('database.connections-pgvector'))) {
+            DB::connection('pgvector')
+                ->statement('DROP EXTENSION IF NOT EXISTS vector');
+
+        }
     }
 };

database/migrations/2023_12_12_150300_create_vector_extension.php

@@ -0,0 +1,26 @@
+<?php
+
+use Illuminate\Database\Migrations\Migration;
+use Illuminate\Support\Facades\DB;
+
+return new class extends Migration {
+    /**
+     * Run the migrations.
+     *
+     * @return void
+     */
+    public function up()
+    {
+        DB::statement('CREATE EXTENSION IF NOT EXISTS vector');
+    }
+
+    /**
+     * Reverse the migrations.
+     *
+     * @return void
+     */
+    public function down()
+    {
+        DB::statement('DROP EXTENSION IF NOT EXISTS vector');
+    }
+};

docker-compose.yml

@@ -22,7 +22,6 @@ services:
     depends_on:
       - app
       - database_testing
-      - vector_database_testing
     build:
       context: ./
       dockerfile: .docker/worker.dockerfile
@@ -66,7 +65,7 @@ services:
 
   # The database
   database:
-    image: postgres:14-alpine
+    image: ghcr.io/biigle/pgvector
     volumes:
       - dbdata:/var/lib/postgresql/data
       - ./:/data
@@ -77,28 +76,7 @@ services:
     ports:
       - "54320:5432"
 
-  vector_database:
-    image: ghcr.io/biigle/pgvector
-    volumes:
-      - vecdbdata:/var/lib/postgresql/data
-      - ./:/data
-    environment:
-      - "POSTGRES_DB=biigle"
-      - "POSTGRES_USER=biigle"
-      - "POSTGRES_PASSWORD=secret"
-    ports:
-      - "54321:5432"
-
   database_testing:
-    image: postgres:14-alpine
-    tmpfs:
-      - /var/lib/postgresql/data
-    environment:
-      - "POSTGRES_DB=biigle"
-      - "POSTGRES_USER=biigle"
-      - "POSTGRES_PASSWORD=secret"
-
-  vector_database_testing:
     image: ghcr.io/biigle/pgvector
     tmpfs:
       - /var/lib/postgresql/data
@@ -109,5 +87,3 @@ services:
 
 volumes:
   dbdata:
-  vecdbdata:
-

phpunit.xml

@@ -29,9 +29,5 @@
         <env name="DB_DATABASE" value="biigle"/>
         <env name="DB_USERNAME" value="biigle"/>
         <env name="DB_PASSWORD" value="secret"/>
-        <env name="VECTOR_DB_HOST" value="vector_database_testing"/>
-        <env name="VECTOR_DB_DATABASE" value="biigle"/>
-        <env name="VECTOR_DB_USERNAME" value="biigle"/>
-        <env name="VECTOR_DB_PASSWORD" value="secret"/>
     </php>
 </phpunit>

resources/assets/js/volumes/components/filterListComponent.vue

@@ -3,6 +3,7 @@
         <strong>with<span v-if="rule.negate">out</span></strong>
         <span v-text="name"></span>
         <strong v-if="dataName" v-text="dataName"></strong>
+        <span class="text-muted" v-text="fileCount"></span>
     </span>
 </template>
 
@@ -18,18 +19,28 @@ export default {
             type: Object,
             required: true,
         },
+        type: {
+            type: String,
+            required: true,
+        },
     },
     data() {
         return {
             name: this.rule.id,
         };
     },
     computed: {
+        fileCount() {
+            let typeForm = this.rule.sequence.length === 1 ? `${this.type}` : `${this.type}s`;
+            return `(${this.rule.sequence.length} ${typeForm})`;
+        },
         dataName() {
             if (this.rule.data) {
-                return this.rule.data.name;
+                if(this.rule.data.name) {
+                    return this.rule.data.name;
+                }
             }
-
+            
             return '';
         },
     },

resources/assets/js/volumes/components/filterTab.vue

@@ -161,11 +161,22 @@ export default {
 
             return null;
         },
+        itemsAreEqual(itemData, ruleData) {
+            // handle Array
+            if (itemData !== null && ruleData !== null) {
+                if (itemData instanceof Array) {
+                    return itemData.length === ruleData.length &&
+                        itemData.every((val, index) => val === ruleData[index]);
+                }
+            }
+            // handle all other types (Objects, null)
+            return itemData === ruleData;
+        },
         hasRule(rule) {
-            return this.rules.findIndex(function (item) {
+            return this.rules.findIndex((item) => {
                 return item.id === rule.id &&
                     item.negate === rule.negate &&
-                    item.data === rule.data;
+                    this.itemsAreEqual(item.data, rule.data);
             }) !== -1;
         },
         addRule(data) {
@@ -176,7 +187,6 @@ export default {
                 data: data,
                 negate: this.negate,
             };
-
             if (this.hasRule(rule)) return;
 
             this.startLoading();