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"load data local infile" in their generated load scripts needs to be changed to "load data infile" and files need to be changed to full path to work with version 5 ("local" command not available in version 5), they suggest using version 5.5.


> From: carlsenbr@mail.nlm.nih.gov
> To: karystig@cs.man.ac.uk
> CC: cshelp@wrist.nlm.nih.gov
> Date: Fri, 15 Jul 2011 13:35:13 -0400
> Subject: RE: EXTERNAL: FW: mysql database populating problem script
>
> George,
>
> The recommended version for UMLS MySQL scripts is 5.5, however we do have some experience running it against 5.0.
>
> I believe the error you are experiencing is related to the use of "load data local infile" within the mysql_tables.sql script. For example:
>
> load data local infile 'MRCOC.RRF' into table MRCOC fields terminated by '|' ESCAPED BY '' lines terminated by @LINE_TERMINATION@
> (@cui1,@aui1,@cui2,@aui2,@sab,@cot,@cof,@coa,@cvf)
> SET CUI1 = @cui1,
> AUI1 = @aui1,
> CUI2 = NULLIF(@cui2,''),
> AUI2 = NULLIF(@aui2,''),
> SAB = @sab,
> COT = @cot,
> COF = NULLIF(@cof,''),
> COA = NULLIF(@coa,''),
> CVF = NULLIF(@cvf,'');
>
> The "local infile" mode doesn't work in 5.0. What this means is that files must be in a path that is accessible to the mysql server itself (no problem if you're running all of this on the same machine).
>
> What you want to do is change all instances of "load data local infile" to " load data infile" and use full paths to filenames (e.g. instead of just 'MRCOC.RRF' use '/full/path/to/MRCOC.RRF').
>
> Remember, the path to the file has to be accessible from the MySQL server itself in this mode, so make sure you're either running the populate_mysql_db.sh script on the same machine as the MySQL server or that the files have been put in a location that is accessible to both the script and the server.
>
> Brian Carlsen
>
>
> -----Original Message-----
> From: NLM Customer Service [mailto:cshelp@wrist.nlm.nih.gov]
> Sent: Wednesday, July 13, 2011 11:21 AM
> To: Carlsen, Brian A
> Cc: wilderv@nlm.nih.gov
> Subject: EXTERNAL: FW: mysql database populating problem script
>
> Brian,
>
> Would appreciate your input with this user. Looks like he needs to update to MySQL Server 5.5. Any other help for him. Please reply to my nlm address.
>
> Thanks, Victoria
>
> [THREAD ID:1-15FSM0]
>
> ------Original Message------
>
> From: karystig@cs.man.ac.uk
> Sent:07/11/2011 13:08:16
> To: Custhelp@mail.nlm.nih.gov
> Subject: mysql database populating problem script
>
> SUBJECT: mysql database populating problem script
> EMAIL: karystig@cs.man.ac.uk
> NAME: GEorge Karystianis
> GROUP: Researcher/Scientist
> STATE:
> COUNTRY: United Kingdom
> FROM: http://www.nlm.nih.gov/research/umls/support.html
> DATE: 07/11/2011
> MESSAGE: Hello,
>
> I am experiencing a problem with UMLS. I am trying to export the sql scripts of metamorphosys into a mysql database-my version of sql is 14.12 Distrib 5.0.26- and when i am at this step:
>
> " % populate_mysql_db.sh &" which is when i am trying to populate the database, i am getting the following error:
>
> "ERROR 1148 (42000) at line 15: The used command is not allowed with this MySQL version ".
>
> Am i doing something wrong or my current version does not match the requirements? If so, could you help give me an indication of where in your shell script i can adjust the command so i can get it to work with my mysql version?
>
> Any help will be appreciated! Thank you very much for your time!
>
> George Karystianis
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Page last modified on July 29, 2011 at 12:45