feat: ontology import/export for neo4j.

oat-sa · Sep 29, 2023 · dee056f · dee056f
1 parent 87b82b5
commit dee056f
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Showing 4 changed files with 127 additions and 48 deletions.
diff --git a/helpers/data/class.GenerisAdapterRdf.php b/helpers/data/class.GenerisAdapterRdf.php
@@ -145,7 +145,7 @@ private function addResource(Graph $graph, core_kernel_classes_Resource $resourc
                 ) {
                     continue;
                 }
-                $graph->add($triple->subject, $triple->predicate, $triple->object);
+                $graph->addResource($triple->subject, $triple->predicate, $triple->object);
             } else {
                 if ($this->isSerializedFile($triple->object)) {
                     continue;

diff --git a/migrations/Version202309111518342234_tao.php b/migrations/Version202309111518342234_tao.php
@@ -0,0 +1,52 @@
+<?php
+
+/*
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; under version 2
+ * of the License (non-upgradable).
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+ *
+ * Copyright (c) 2023(original work) Open Assessment Technologies SA;
+ */
+
+declare(strict_types=1);
+
+namespace oat\tao\migrations;
+
+use Doctrine\DBAL\Schema\Schema;
+use oat\tao\scripts\SyncModels;
+use oat\tao\scripts\tools\migrations\AbstractMigration;
+
+/**
+ * phpcs:disable Squiz.Classes.ValidClassName
+ */
+final class Version202309111518342234_tao extends AbstractMigration
+{
+    public function getDescription(): string
+    {
+        return 'Update Ontology models';
+    }
+
+    public function up(Schema $schema): void
+    {
+        $this->addReport(
+            $this->propagate(new SyncModels())([])
+        );
+    }
+
+    public function down(Schema $schema): void
+    {
+        $this->throwIrreversibleMigrationException(
+            'The models should be updated via `SyncModels` script after reverting their RDF definitions.'
+        );
+    }
+}
diff --git a/scripts/tools/MigrateSqlToNeo4j.php b/scripts/tools/MigrateSqlToNeo4j.php
@@ -32,6 +32,7 @@
 use oat\oatbox\extension\script\ScriptAction;
 use oat\oatbox\reporting\Report;
 use oat\tao\model\TaoOntology;
+use WikibaseSolutions\CypherDSL\Query;
 
 /**
  * php -dmemory_limit=1G index.php 'oat\tao\scripts\tools\MigrateSqlToNeo4j' -u -i -s 10000 -n 10000 -vvv
@@ -242,12 +243,11 @@ public function extractDataFromSqlStorage(int $chunkSize): \Generator
      */
     public function loadNTripleToNeo4j($neo4j, string $nTriple, int $neo4jChunkSize): void
     {
-        $nTriple = $this->escapeTriple($nTriple);
-
         $result = $neo4j->run(<<<CYPHER
-CALL n10s.rdf.import.inline('${nTriple}',"N-Triples",{commitSize:${neo4jChunkSize}}) YIELD terminationStatus, extraInfo
+CALL n10s.rdf.import.inline(\$nTriple,"N-Triples",{commitSize:${neo4jChunkSize}}) YIELD terminationStatus, extraInfo
 RETURN terminationStatus, extraInfo
-CYPHER
+CYPHER,
+        ['nTriple' => $nTriple]
         );
 
         $responseMessage = $result->first();
@@ -263,31 +263,6 @@ public function loadNTripleToNeo4j($neo4j, string $nTriple, int $neo4jChunkSize)
         $this->logInfo('Chunk of triples successfully loaded.');
     }
 
-    public function escapeTriple(string $nTriple): string
-    {
-        $escapeCharacters = [
-            '\\\\' => '\\\\\\\\', //Escape double slash
-            '\"' => '\\\\"', // Escaped slash in escaped double quote
-            '\n' => '\\\\n', // Escaped slash in EOL
-            '\r' => '\\\\r', // Escaped slash in carriage return
-            '\t' => '\\\\t', // Escaped slash in horizontal tab
-            "'" => "\'", //Escape single quote
-        ];
-
-        $escapeList = [];
-        foreach ($escapeCharacters as $needle => $replacement) {
-            if (strpos($nTriple, $needle) !== false) {
-                $escapeList[$needle] = $replacement;
-            }
-        }
-
-        if (!empty($escapeList)) {
-            $nTriple = str_replace(array_keys($escapeList), array_values($escapeList), $nTriple);
-        }
-
-        return $nTriple;
-    }
-
     protected function provideOptions(): array
     {
         return [
@@ -354,10 +329,47 @@ protected function run(): Report
             foreach ($nTripleList as $nTriple) {
                 $this->loadNTripleToNeo4j($neo4j, $nTriple, $neo4jChunkSize);
             }
+
+            $this->addSystemLabel($neo4j, $sqlChunkSize, $neo4jChunkSize);
         } catch (\Throwable $e) {
             return Report::createError($e->getMessage());
         }
 
         return Report::createSuccess('Data transfer finished successfully.');
     }
+
+    private function addSystemLabel($neo4j, int $sqlChunkSize, int $neo4jChunkSize)
+    {
+        $sql = $this->getSqlAdapter();
+
+            /** @var \Doctrine\DBAL\ForwardCompatibility\Result $idResult */
+        $result = $sql->query(<<<'SQL'
+                SELECT subject
+                    FROM statements
+                    WHERE modelid <> 1
+                    GROUP BY subject;
+SQL);
+
+        $subjectList = [];
+        while ($r = $result->fetchColumn()) {
+            $subjectList[] = $r;
+
+            if (count($subjectList) >= $neo4jChunkSize) {
+                $systemNode = Query::node('Resource');
+                $query = Query::new()->match($systemNode)
+                    ->where($systemNode->property('uri')->in($subjectList))
+                    ->set($systemNode->labeled('System'));
+                $neo4j->runStatement($query);
+                $subjectList = [];
+            }
+        }
+
+        if (!empty($subjectList)) {
+            $systemNode = Query::node('Resource');
+            $query = Query::new()->match($systemNode)
+                ->where($systemNode->property('uri')->in($subjectList))
+                ->set($systemNode->labeled('System'));
+            $neo4j->run($query->build());
+        }
+    }
 }
diff --git a/scripts/update/OntologyUpdater.php b/scripts/update/OntologyUpdater.php
@@ -23,34 +23,23 @@
 namespace oat\tao\scripts\update;
 
 use AppendIterator;
-use oat\generis\model\kernel\persistence\file\FileModel;
-use oat\generis\model\data\ModelManager;
-use helpers_RdfDiff;
-use core_kernel_persistence_smoothsql_SmoothModel;
-use common_persistence_SqlPersistence;
 use common_ext_ExtensionsManager;
-use core_kernel_persistence_smoothsql_SmoothIterator;
+use helpers_RdfDiff;
+use oat\generis\model\data\Model;
+use oat\generis\model\data\ModelManager;
+use oat\generis\model\kernel\persistence\file\FileModel;
 use oat\tao\model\extension\ExtensionModel;
 
 class OntologyUpdater
 {
     public static function syncModels()
     {
         $currentModel = ModelManager::getModel();
-        $modelIds = array_diff($currentModel->getReadableModels(), ['1']);
-
-        $persistence = common_persistence_SqlPersistence::getPersistence('default');
 
-        $smoothIterator = new core_kernel_persistence_smoothsql_SmoothIterator($persistence, $modelIds);
-
-        $nominalModel = new AppendIterator();
-        foreach (common_ext_ExtensionsManager::singleton()->getInstalledExtensions() as $ext) {
-            $nominalModel->append(new ExtensionModel($ext));
-        }
-        $langModel = \tao_models_classes_LanguageService::singleton()->getLanguageDefinition();
-        $nominalModel->append($langModel);
+        $existingTriples = self::getCurrentTriples($currentModel);
+        $nominalTriples = self::getNominalTriples();
 
-        $diff = helpers_RdfDiff::create($smoothIterator, $nominalModel);
+        $diff = helpers_RdfDiff::create($existingTriples, $nominalTriples);
         self::logDiff($diff);
 
         $diff->applyTo($currentModel);
@@ -82,4 +71,30 @@ protected static function logDiff(\helpers_RdfDiff $diff)
         FileModel::toFile($path . DIRECTORY_SEPARATOR . 'add.rdf', $diff->getTriplesToAdd());
         FileModel::toFile($path . DIRECTORY_SEPARATOR . 'remove.rdf', $diff->getTriplesToRemove());
     }
+
+    public static function getNominalTriples(): \Traversable
+    {
+        $nominalModel = new AppendIterator();
+        foreach (common_ext_ExtensionsManager::singleton()->getInstalledExtensions() as $ext) {
+            $nominalModel->append(new ExtensionModel($ext));
+        }
+        $langModel = \tao_models_classes_LanguageService::singleton()->getLanguageDefinition();
+        $nominalModel->append($langModel);
+        return $nominalModel;
+    }
+
+    public static function getCurrentTriples(Model $currentModel): \Traversable
+    {
+        return new \CallbackFilterIterator(
+                $currentModel->getRdfInterface()->getIterator(),
+            function (\core_kernel_classes_Triple $item) {
+                $isAutomaticIncludeRole = $item->subject === 'http://www.tao.lu/Ontologies/TAO.rdf#GlobalManagerRole'
+                    && $item->predicate === 'http://www.tao.lu/Ontologies/generis.rdf#includesRole';
+                $isGrantAccess = $item->predicate === 'http://www.tao.lu/Ontologies/taoFuncACL.rdf#GrantAccess';
+
+
+                return !$isGrantAccess && !$isAutomaticIncludeRole;
+            }
+        );
+    }
 }