Magento 2 Reindex Issue – MySQL Configuration Guide

The catalog_product_index_eav table has a foreign key contraint named

FK_CAT_PRD_IDX_EAV_ENTT_ID_CAT_PRD_ENTT_ENTT_ID

Looking at this table's definition

CREATE TABLE `catalog_product_index_eav` (
  `entity_id` int(10) unsigned NOT NULL DEFAULT '0' COMMENT 'Entity ID',
  `attribute_id` smallint(5) unsigned NOT NULL DEFAULT '0' COMMENT 'Attribute ID',
  `store_id` smallint(5) unsigned NOT NULL DEFAULT '0' COMMENT 'Store ID',
  `value` int(10) unsigned NOT NULL DEFAULT '0' COMMENT 'Value',
  PRIMARY KEY (`entity_id`,`attribute_id`,`store_id`,`value`),
  KEY `IDX_CATALOG_PRODUCT_INDEX_EAV_ENTITY_ID` (`entity_id`),
  KEY `IDX_CATALOG_PRODUCT_INDEX_EAV_ATTRIBUTE_ID` (`attribute_id`),
  KEY `IDX_CATALOG_PRODUCT_INDEX_EAV_STORE_ID` (`store_id`),
  KEY `IDX_CATALOG_PRODUCT_INDEX_EAV_VALUE` (`value`),
  CONSTRAINT `FK_CATALOG_PRODUCT_INDEX_EAV_STORE_ID_CORE_STORE_STORE_ID` FOREIGN KEY (`store_id`) REFERENCES `core_store` (`store_id`) ON DELETE CASCADE ON UPDATE CASCADE,
  CONSTRAINT `FK_CAT_PRD_IDX_EAV_ATTR_ID_EAV_ATTR_ATTR_ID` FOREIGN KEY (`attribute_id`) REFERENCES `eav_attribute` (`attribute_id`) ON DELETE CASCADE ON UPDATE CASCADE,
  CONSTRAINT `FK_CAT_PRD_IDX_EAV_ENTT_ID_CAT_PRD_ENTT_ENTT_ID` FOREIGN KEY (`entity_id`) REFERENCES `catalog_product_entity` (`entity_id`) ON DELETE CASCADE ON UPDATE CASCADE
) ENGINE=InnoDB DEFAULT CHARSET=utf8 COMMENT='Catalog Product EAV Index Table';

we can see the foreign key definition is

CONSTRAINT `FK_CAT_PRD_IDX_EAV_ENTT_ID_CAT_PRD_ENTT_ENTT_ID` 
FOREIGN KEY (`entity_id`) 
REFERENCES `catalog_product_entity` (`entity_id`) 
ON DELETE CASCADE ON UPDATE CASCADE

This means for every entity_id row in catalog_product_index_eav, there needs to be an identical, corresponding entity_id value in catalog_product_entity.

The root of your problem is for some reason (either a rouge extension, errors caused by randomly typing in SQL from the internet, or performing data updates with disabled indexes), Magento's indexing attempts to update data in catalog_product_index_eav that violates this rule. The next step is identifying what Magento's doing so you can fix the data.

If we look at your call stack, this looks like a good place to start debugging

#10 app/code/core/Mage/Catalog/Model/Resource/Product/Indexer/Eav/Abstract.php(54): 
Mage_Index_Model_Resource_Abstract->syncData()

Jumping to that source file, we see the following bit of code

public function syncData()
{
    $this->beginTransaction();
    try {
        /**
         * Can't use truncate because of transaction
         */
        $this->_getWriteAdapter()->delete($this->getMainTable());
        $this->insertFromTable($this->getIdxTable(), $this->getMainTable(), false);
        $this->commit();
    } catch (Exception $e) {
        $this->rollBack();
        throw $e;
    }
    return $this;
}

As part of its indexing process, Magento tries to sync data from an "index table" (getIdxTable), to a "source" (getMainTable) table.

public function insertFromTable($sourceTable, $destTable, $readToIndex = true)
{
    //...
}

For this particular index, the index table is catalog_product_index_eav_idx, and the source table is catalog_product_index_eav.

Note: Be careful with your terminology around here, things are confusingly named. The "Source" table is the table we're copying to. (I believe it's called the source table because it's the "source" a normal Magento system will query from when it needs information)

So, Magento is trying to sync a row from catalog_product_index_eav_idx to the table catalog_product_index_eav. However, this causes the previously mentioned foreign key error. This leads us to two possible conclusions

1. The catalog_product_index_eav_idx has entity_id rows that do not exist in catalog_product_entity.

2. The catalog_product_index_eav table has (through previous manipulation with index checks turned off) entity_id rows that do not exist in catalog_product_entity.

So, your mission here is to figure out which entity_id rows in catalog_product_index_eav and catalog_product_index_eav_idx don't exist in catalog_product_entity, and manually delete said rows (from catalog_product_index_eav and catalog_product_index_eav_idx).

If it were me, and my catalog_product_entity table wasn't too large, I'd start with the following queries (these are untested, as I don't have any Magento tables with the above invalid data states)

SELECT * 
FROM catalog_product_index_eav_idx 
WHERE NOT (entity_id IN (SELECT entity_id from catalog_product_entity));

SELECT * FROM catalog_product_index_eav 
WHERE NOT (entity_id IN (SELECT entity_id from catalog_product_entity));

Good luck!

The error is because the transaction is reaching its timeout period. If you did not set this in your my.cnf the default is 50 seconds I would highly recommend you look at your sever settings to ensure that they are optimized for your database using tools such as MySQLTuner

I have the innodb_lock_wait_timeout set to 7200 (2 hours) in a store with 500k products with 2 store views.

Example to add or change in my.cnf

innodb_lock_wait_timeout = 7200

DO NOT TRUNCATE.... yet

When you "moved around or reorganised a category" Magento will keep the references to these original links (hence the massive amount of links and 4 store views as well) and redirect them for visitors / bots / search engines that have book marked or indexed these pages.This can negatively affect your SEO, when you truncate they will receive a error 404 message. My personal recommendation is BEFORE doing major changes to the structure, ensure that nothing of the sort has been done for at least a month, then truncate then do your restructuring. This will cut down enormously on the size of your URL Rewrites

Since you've already re-arranged your categories, the best thing to do now is wait for a month to give visitors / bots / search engines the time to update the links --- then purge.

Also checkout:Magento core_url_rewrite table excessively large