[BioSQL-l] Possible Mysql 5.x bug

[Hilmar Lapp]

Hi James,

thanks for reporting this. Sebastian Bassi beat you to it, though,  
and it has actually been fixed in svn, and is also fixed in the 1.0.0  
release.

BioSQL is meanwhile on svn; the anonymous cvs server is still up, but  
doesn't get updated since the switch-over to svn. Instructions for  
downloading from svn and download location of the 1.0.0 release are  
on the BioSQL wiki at http://biosql.org.

Let us know if you encounter any difficulties. And great that you're  
finding the project useful!

	-hilmar

On Mar 10, 2008, at 3:27 PM, James Swetnam wrote:

> First off, thank you very much to the developers for creating and
> maintaining such a useful and interesting project.  I think I have
> found a small syntactical bug; as a caveat, however, I am not a
> database developer and have very little experience in these matters.
>    I do know how to read documentation though, which I've relied  
> heavily
>    on to write this email.
>    As per the biopython setup tutorial I'm attempting to run the  
> biosqldb-
>    mysql.sql file on Mac OS X Leopard.  Here is my mysql version  
> string:
>    cardozo13:sql james$ mysql -V
>    mysql  Ver 14.12 Distrib 5.0.54-20071214, for apple-darwin9.1.0
>    (powerpc) using  EditLine wrapper
>    And my procedure (after grabbing the biosql source via CVS).
>    cardozo13:sql james$ mysqladmin -u root -p create bioseqdb
>    Enter password:
>    cardozo13:sql james$ mysql -u root bioseqdb -p < biosqldb-
>    mysql.sqlEnter password:
>    ERROR 1064 (42000) at line 169: You have an error in your SQL  
> syntax;
>    check the manual that corresponds to your MySQL server version  
> for the
>    right syntax to use near '--CREATE INDEX ontrel_subjectid ON
>    term_relationship(subject_term_id)' at line 1
>    Interesting.  Let's take a look at line 169:
>
>    --CREATE INDEX ontrel_subjectid ON term_relationship 
> (subject_term_id);
>
>    And an excerpt from the documentation for my version of MySQL (5.0
>    reference manual), section 1.8.5.6. '--' as the Start of a Comment:
>
>    Standard SQL uses “--” as a start-comment sequence. MySQL Server  
> uses
>    “#” as the start comment character. MySQL Server 3.23.3 and up also
>    supports a variant of the “--” comment style. That is, the “--”  
> start-
>    comment sequence must be followed by a space (or by a control
>    character such as a newline). The space is required to prevent
>    problems with automatically generated SQL queries that use  
> constructs
>    such as the following, where we automatically insert the value  
> of the
>    payment for payment:
>
>    OK. So after replacing all the lines in which -- is not followed  
> by a
>    space (thank you regexps), it works beautifully.
>
>    cardozo13:sql james$ mysql -u root bioseqdb -p < biosqldb-mysql.sql
>    Enter password:
>
>    Should this change be implemented?  Or am i missing something?
>
>    James Swetnam
>    Research Technician
>    New York University School of Medicine
>
>
>
>
>
>
>
> - Done.
>
>
>
> ---------- Forwarded message ----------
> From: "James Swetnam" <jswetnam at gmail.com>
> To: biosql-l-request at lists.open-bio.org
> Date: Thu, 6 Mar 2008 18:10:07 -0500
> Subject: Comment Syntax bug Generates error on
> Hello.
>
> First off, thank you very much to the developers for creating and
> maintaining such a useful and interesting project.  I think I have
> found a small syntactical bug; as a caveat, however, I am not a
> database developer and have very little experience in these matters.
> I do know how to read documentation though, which I've relied heavily
> on to write this email.
>
> As per the biopython setup tutorial I'm attempting to run the  
> biosqldb-
> mysql.sql file on Mac OS X Leopard.  Here is my mysql version string:
>
> cardozo13:sql james$ mysql -V
> mysql  Ver 14.12 Distrib 5.0.54-20071214, for apple-darwin9.1.0
> (powerpc) using  EditLine wrapper
>
> And my procedure (after grabbing the biosql source via CVS).
>
> cardozo13:sql james$ mysqladmin -u root -p create bioseqdb
> Enter password:
> cardozo13:sql james$ mysql -u root bioseqdb -p < biosqldb-
> mysql.sqlEnter password:
> ERROR 1064 (42000) at line 169: You have an error in your SQL syntax;
> check the manual that corresponds to your MySQL server version for the
> right syntax to use near '--CREATE INDEX ontrel_subjectid ON
> term_relationship(subject_term_id)' at line 1
>
> Interesting.  Let's take a look at line 169:
>
> --CREATE INDEX ontrel_subjectid ON term_relationship(subject_term_id);
>
> And an excerpt from the documentation for my version of MySQL (5.0
> reference manual), section 1.8.5.6. '--' as the Start of a Comment:
>
> Standard SQL uses “--” as a start-comment sequence. MySQL Server uses
> “#” as the start comment character. MySQL Server 3.23.3 and up also
> supports a variant of the “--” comment style. That is, the “--” start-
> comment sequence must be followed by a space (or by a control
> character such as a newline). The space is required to prevent
> problems with automatically generated SQL queries that use constructs
> such as the following, where we automatically insert the value of the
> payment for payment:
>
> OK. So after replacing all the lines in which -- is not followed by a
> space (thank you regexps), it works beautifully.
>
> cardozo13:sql james$ mysql -u root bioseqdb -p < biosqldb-mysql.sql
> Enter password:
>
> Should this change be implemented?  Or am i missing something?
>
> James Swetnam
> Research Technician
> New York University School of Medicine
>
>
>
>
>
>
>
> Reply
> 		
> Forward
> 		
> 	
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================