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UMLSINSTALL"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 |