MYSQL代碼創建傳遞關閉表失敗

Question

我正在使用當前的SNOMED數據和示例，並且想創建一個傳遞閉包表，但是mysql5.6默認服務器設置中的某些操作失敗。

對於那些不知道的人，SNOMED是醫學數據庫。 有210萬個關系和446697個概念。 該查詢在第二部分停滯了-因此我猜想它的內存不足。 但是我需要調整哪些設置？ join_buffer_size？

這是代碼：

DELIMITER ;;
CREATE DEFINER=`snomed`@`localhost` PROCEDURE `createTc`()
BEGIN
    drop table if exists tc;

    CREATE TABLE tc (
        source BIGINT UNSIGNED NOT NULL ,
        dest BIGINT UNSIGNED NOT NULL
        ) ENGINE = InnoDB CHARSET=utf8;
    insert into tc (source, dest)
        select distinct rel.sourceid, rel.destinationid
        from rf2_ss_relationships rel
        inner join rf2_ss_concepts con
            on rel.sourceid = con.id and con.active = 1
        where rel.typeid = 116680003 # IS A relationship
        and rel.active = 1;
    REPEAT
        insert into tc (source, dest)
            select distinct b.source, a.dest
            from tc a
            join tc b on a.source = b.dest
            left join tc c on c.source = b.source and c.dest = a.dest
            where c.source is null;
        set @x = row_count();
        select concat('Inserted ', @x);
    UNTIL @x = 0 END REPEAT;
    create index idx_tc_source on tc (source);
    create index idx_tc_dest on tc (dest);
END;;
DELIMITER ;
CREATE TABLE `rf2_ss_relationships` (
  `id` bigint(20) unsigned NOT NULL,
  `effectiveTime` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
  `active` tinyint(4) DEFAULT '1',
  `moduleId` bigint(20) unsigned NOT NULL,
  `sourceId` bigint(20) unsigned NOT NULL,
  `destinationId` bigint(20) unsigned NOT NULL,
  `relationshipGroup` bigint(20) unsigned NOT NULL,
  `typeId` bigint(20) unsigned NOT NULL,
  `characteristicTypeId` bigint(20) unsigned NOT NULL,
  `modifierId` bigint(20) unsigned NOT NULL,
  PRIMARY KEY (`id`,`effectiveTime`),
  KEY `moduleId_idx` (`moduleId`),
  KEY `sourceId_idx` (`sourceId`),
  KEY `destinationId_idx` (`destinationId`),
  KEY `relationshipGroup_idx` (`relationshipGroup`),
  KEY `typeId_idx` (`typeId`),
  KEY `characteristicTypeId_idx` (`characteristicTypeId`),
  KEY `modifierId_idx` (`modifierId`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;

 CREATE TABLE `rf2_ss_concepts` (
  `id` bigint(20) unsigned NOT NULL,
  `effectiveTime` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
  `active` tinyint(4) DEFAULT NULL,
  `moduleId` bigint(20) unsigned NOT NULL,
  `definitionStatusId` bigint(20) unsigned NOT NULL,
  PRIMARY KEY (`id`,`effectiveTime`),
  KEY `moduleId_idx` (`moduleId`),
  KEY `definitionStatusId_idx` (`definitionStatusId`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;

Answer 1

我不知道這是否是最好的答案，但是它確實可以工作...我更改了create table語法以在創建時添加索引-而不是在完成之后。 我將innodb_buffer_pool_size = 8G的mysqld設置更改為

    CREATE TABLE tc (
    source BIGINT UNSIGNED NOT NULL ,
    dest BIGINT UNSIGNED NOT NULL,
    KEY source_idx (source),
    KEy dest_idx (dest)
    ) ENGINE = InnoDB CHARSET=utf8;

甚至在帶SSD的i7 mac上，執行速度仍然不快，但確實有效，並且傳遞關閉表為5180059行....

mysql> call createTc;
+-------------------------+
| concat('Inserted ', @x) |
+-------------------------+
| Inserted 654161         |
+-------------------------+
1 row in set (1 min 55.13 sec)

+-------------------------+
| concat('Inserted ', @x) |
+-------------------------+
| Inserted 1752024        |
+-------------------------+
1 row in set (3 min 5.60 sec)

+-------------------------+
| concat('Inserted ', @x) |
+-------------------------+
| Inserted 2063816        |
+-------------------------+
1 row in set (10 min 42.07 sec)

+-------------------------+
| concat('Inserted ', @x) |
+-------------------------+
| Inserted 275904         |
+-------------------------+
1 row in set (28 min 5.49 sec)

+-------------------------+
| concat('Inserted ', @x) |
+-------------------------+
| Inserted 280            |
+-------------------------+
1 row in set (46 min 29.78 sec)

+-------------------------+
| concat('Inserted ', @x) |
+-------------------------+
| Inserted 0              |
+-------------------------+
1 row in set (1 hour 5 min 20.05 sec)

Query OK, 0 rows affected (1 hour 5 min 20.05 sec)

Answer 2

我使用這種遞歸方法。 在閱讀關系時，我已經將所有直接后代添加到概念對象的列表中（我使用了休眠），因此它們可用。

然后，通過瀏覽概念列表來啟動此遞歸函數。 參見示例。 它遍歷所有直接父母的清單中的每個概念：

for (Sct2Concept c : concepts.values()) {
    for(Sct2Relationship parentRelation : c.getChildOfRelationships()){
        addParentToList(concepts, sct2TransitiveClosureList, parentRelation, c);
    }
}

如您所見，TransitiveClosure內存存儲區是一個Set，以便在智能且非常成熟的Java庫內部代碼上檢查唯一值。

private void addParentToList(Map<String, Sct2Concept> concepts, Set<Sct2TransitiveClosure> sct2TransitiveClosureList, Sct2Relationship parentRelation, Sct2Concept c){
        if(!parentRelation.isActive())
            return;
        Sct2TransitiveClosure tc = new Sct2TransitiveClosure(parentRelation.getDestinationSct2Concept().getId(), c.getId());
        if(sct2TransitiveClosureList.add(tc)){
            Sct2Concept s = concepts.get(Long.toString(tc.getParentId()));
            for(Sct2Relationship newParentRelation : s.getChildOfRelationships()){
                addParentToList(concepts, sct2TransitiveClosureList, newParentRelation, c);
        }
    }
}