Solution :

       18th October 2007

To start: as of the latest MySQL, syntax presented in the title is not possible. But there are several very easy ways to accomplish what is expected using existing functionality.

There are 3 possible solutions: using INSERT IGNORE, REPLACE, or INSERT … ON DUPLICATE KEY UPDATE.

Imagine we have a table:

CREATE TABLE `transcripts` (
`ensembl_transcript_id` varchar(20) NOT NULL,
`transcript_chrom_start` int(10) unsigned NOT NULL,
`transcript_chrom_end` int(10) unsigned NOT NULL,
PRIMARY KEY (`ensembl_transcript_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;

Now imagine that we have an automatic pipeline importing transcripts meta-data from Ensembl, and that due to various reasons the pipeline might be broken at any step of execution. Thus, we need to ensure two things: 1) repeated executions of the pipeline will not destroy our database, and 2) repeated executions will not die due to ‘duplicate primary key’ errors.

Method 1: using REPLACE

It’s very simple:

REPLACE INTO `transcripts`
SET `ensembl_transcript_id` = ‘ENSORGT00000000001′,
`transcript_chrom_start` = 12345,
`transcript_chrom_end` = 12678;

If the record exists, it will be overwritten; if it does not yet exist, it will be created. However, using this method isn’t efficient for our case: we do not need to overwrite existing records, it’s fine just to skip them.

Method 2: using INSERT IGNORE Also very simple:

INSERT IGNORE INTO `transcripts`
SET `ensembl_transcript_id` = ‘ENSORGT00000000001′,
`transcript_chrom_start` = 12345,
`transcript_chrom_end` = 12678;

Here, if the ‘ensembl_transcript_id’ is already present in the database, it will be silently skipped (ignored). (To be more precise, here’s a quote from MySQL reference manual: “If you use the IGNORE keyword, errors that occur while executing the INSERT statement are treated as warnings instead. For example, without IGNORE, a row that duplicates an existing UNIQUE index or PRIMARY KEY value in the table causes a duplicate-key error and the statement is aborted.”.) If the record doesn’t yet exist, it will be created.

This second method has several potential weaknesses, including non-abortion of the query in case any other problem occurs (see the manual). Thus it should be used if previously tested without the IGNORE keyword.

There is one more option: to use INSERT … ON DUPLICATE KEY UPDATE syntax, and in the UPDATE part just do nothing do some meaningless (empty) operation, like calculating 0+0 (Geoffray suggests doing the id=id assignment for the MySQL optimization engine to ignore this operation). Advantage of this method is that it only ignores duplicate key events, and still aborts on other errors.

As a final notice: this post was inspired by Xaprb. I’d also advise to consult his other post on writing flexible SQL queries.