[BioPython] BioSQL documentation for Biopython

[Hilmar Lapp]

Interesting. Apparently MySQL needs a space after the double-dash  
comment prefix:

<quote>In MySQL, the “-- ” (double-dash) comment style requires the  
second dash to be followed by at least one whitespace or control  
character (such as a space, tab, newline, and so on). This syntax  
differs slightly from standard SQL comment syntax [...].</quote><sigh/>

If you add that space, i.e., change the line:

--CREATE INDEX ontrel_subjectid ON term_relationship(subject_term_id);

to

-- CREATE INDEX ontrel_subjectid ON term_relationship(subject_term_id);

and do the same for all other lines where this occurs, does it work  
then?

I've also updated the MySQL schema on svn:

http://code.open-bio.org/svnweb/index.cgi/biosql/view/biosql-schema/ 
trunk/sql/biosqldb-mysql.sql

BTW the reason this hasn't come up before is that most everyone uses  
the mysql command line client to instantiate the schema, which  
ignores lines starting with '--'.

	-hilmar



On Feb 22, 2008, at 6:45 PM, Sebastian Bassi wrote:

> On Fri, Feb 22, 2008 at 1:21 AM, Hilmar Lapp <hlapp at gmx.net> wrote:
>>  Could some Biopythonist check this material whether or not it still
>>  has any relevance, and whether there are any errors?
>
> I've tried to import the schema (biosqldb-mysql.sql) into my MySQL
> server (5.0.45-Debian_1ubuntu3-log) and got this:
>
> Error
> SQL query:
> -- CONFIG: you may want to add this for mysql because MySQL often  
> is broken
> -- with respect to using the composite index for the initial keys
>  - - CREATE INDEX ontrel_subjectid ON term_relationship(
> subject_term_id
> );
>
> MySQL said:
> #1064 - 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
>
> So I tried with "compatibility with SQL323" (option in the
> phpmyadmin), but got the same result.
>
>
> -- 
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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