Merge magento-partners/magento2ce#65.

Author: Volodymyr Kublytskyi

app/code/Magento/Catalog/Model/Indexer/Category/Flat/AbstractAction.php

@@ -369,25 +369,55 @@ protected function getAttributeValues($entityIds, $storeId)
         }
         $values = [];
 
-        foreach ($entityIds as $entityId) {
-            $values[$entityId] = [];
+        $linkIds = $this->getLinkIds($entityIds);
+        foreach ($linkIds as $linkId) {
+            $values[$linkId] = [];
         }
+
         $attributes = $this->getAttributes();
         $attributesType = ['varchar', 'int', 'decimal', 'text', 'datetime'];
+        $linkField = $this->getCategoryMetadata()->getLinkField();
         foreach ($attributesType as $type) {
             foreach ($this->getAttributeTypeValues($type, $entityIds, $storeId) as $row) {
-                if (isset($row[$this->getCategoryMetadata()->getLinkField()]) && isset($row['attribute_id'])) {
+                if (isset($row[$linkField]) && isset($row['attribute_id'])) {
                     $attributeId = $row['attribute_id'];
                     if (isset($attributes[$attributeId])) {
                         $attributeCode = $attributes[$attributeId]['attribute_code'];
-                        $values[$row[$this->getCategoryMetadata()->getLinkField()]][$attributeCode] = $row['value'];
+                        $values[$row[$linkField]][$attributeCode] = $row['value'];
                     }
                 }
             }
         }
+
         return $values;
     }
 
+    /**
+     * Translate entity ids into link ids
+     *
+     * Used for rows with no EAV attributes set.
+     *
+     * @param array $entityIds
+     * @return array
+     */
+    private function getLinkIds(array $entityIds)
+    {
+        $linkField = $this->getCategoryMetadata()->getLinkField();
+        if ($linkField === 'entity_id') {
+            return $entityIds;
+        }
+
+        $select = $this->connection->select()->from(
+            ['e' => $this->connection->getTableName($this->getTableName('catalog_category_entity'))],
+            [$linkField]
+        )->where(
+            'e.entity_id IN (?)',
+            $entityIds
+        );
+
+        return $this->connection->fetchCol($select);
+    }
+
     /**
      * Return attribute values for given entities and store of specific attribute type
      *

app/code/Magento/Catalog/Model/Indexer/Category/Flat/Action/Full.php

@@ -64,18 +64,22 @@ protected function populateFlatTables(array $stores)
             }
             /** @TODO Do something with chunks */
             $categoriesIdsChunks = array_chunk($categoriesIds[$store->getRootCategoryId()], 500);
+
             foreach ($categoriesIdsChunks as $categoriesIdsChunk) {
                 $attributesData = $this->getAttributeValues($categoriesIdsChunk, $store->getId());
+                $linkField = $this->categoryMetadata->getLinkField();
+
                 $data = [];
                 foreach ($categories[$store->getRootCategoryId()] as $category) {
-                    if (!isset($attributesData[$category[$this->categoryMetadata->getLinkField()]])) {
+                    if (!isset($attributesData[$category[$linkField]])) {
                         continue;
                     }
                     $category['store_id'] = $store->getId();
                     $data[] = $this->prepareValuesToInsert(
-                        array_merge($category, $attributesData[$category[$this->categoryMetadata->getLinkField()]])
+                        array_merge($category, $attributesData[$category[$linkField]])
                     );
                 }
+
                 $this->connection->insertMultiple(
                     $this->addTemporaryTableSuffix($this->getMainStoreTable($store->getId())),
                     $data

app/code/Magento/Catalog/Model/Indexer/Category/Flat/Action/Rows.php

@@ -69,22 +69,24 @@ public function reindex(array $entityIds = [], $useTempTable = false)
                 $categoriesIdsChunk = $this->filterIdsByStore($categoriesIdsChunk, $store);
 
                 $attributesData = $this->getAttributeValues($categoriesIdsChunk, $store->getId());
+                $linkField = $this->categoryMetadata->getLinkField();
                 $data = [];
                 foreach ($categoriesIdsChunk as $categoryId) {
-                    if (!isset($attributesData[$categoryId])) {
-                        continue;
-                    }
-
                     try {
                         $category = $this->categoryRepository->get($categoryId);
                     } catch (NoSuchEntityException $e) {
                         continue;
                     }
 
+                    $categoryData = $category->getData();
+                    if (!isset($attributesData[$categoryData[$linkField]])) {
+                        continue;
+                    }
+
                     $data[] = $this->prepareValuesToInsert(
                         array_merge(
-                            $category->getData(),
-                            $attributesData[$categoryId],
+                            $categoryData,
+                            $attributesData[$categoryData[$linkField]],
                             ['store_id' => $store->getId()]
                         )
                     );