[Gmod-help] FlyBase Chado mapping tables

[Josh Goodman]

Hi Dave,

The SQL is originally from an internal FlyBase Trac wiki itself so the 
formatting isn't great there either.  I'm using a perl program to download 
them and convert them to this wiki page, removing a bunch of internal 
project management rubbish in the process.  I'll look into using one of 
the perl SQL parsers to spiff up the formatting tomorrow.

Do you have any feeling for how hard it would be to install the wikimedia 
plugin that lets you do something like this?

<source lang="sql">
SELECT * 
FROM books
WHERE price > 100.00
ORDER BY title;
</source>

That may make things easier.

Thanks,
Josh

On Thu, 5 Jun 2008, Dave Clements wrote:

> Josh, Hilmar,
> 
> I am at a conference and I had to *buy* internet access.  I feel icky (and
> more than a bit spoiled).
> 
> Josh, this is not what I was picturing, but I agree with Hilmar - it is darn
> useful.  I don't think the format lends itself to anchors (dangit).
> 
> How hard is it to indent the SQL, rather than present it as one continuous
> string of text.  I'm not suggesting that anyone manually indent it, but I'm
> wondering if the text was originally indented.  Also, some of the queries
> select many columns and it is not always immediately obvious which one is
> the field in question.  In such cases, is it worth the *manual* effort to
> bold the column?
> 
> Also, once the page has settled I'd be happy to manually update the few long
> lines that don't have embedded spaces so that the SQL resizes with the
> window.
> 
> Thanks for doing this,
> 
> Dave C
> 
> 
> On Thu, Jun 5, 2008 at 9:11 AM, Josh Goodman <jogoodma at indiana.edu> wrote:
> 
> > Hi Hilmar,
> >
> > Thanks for your message.  Its good to see that you think they would be
> > useful.  I'll continue putting up more mapping docs and will collapse them
> > into one page in order to simplify things.
> >
> > Cheers,
> > Josh
> >
> >
> > Hilmar Lapp wrote:
> >
> >> Hi Josh,
> >>
> >> Dave is at a conference starting this afternoon and so it may take a
> >> little until he gets to respond, so I'll just chime in briefly.
> >>
> >> On Jun 4, 2008, at 4:16 PM, Josh Goodman wrote:
> >>
> >>  I put up a rough draft of the FlyBase Chado page (
> >>> http://gmod.org/wiki/index.php/FlyBase_Chado) along with a rough
> >>> approximation of what the field mapping docs will look like (
> >>> http://gmod.org/wiki/index.php/FlyBase_Gene_Report).
> >>>
> >>
> >> This looks like an extremely useful piece of documentation! It also shows
> >> on the side how you are organizing the data, and what vocabulary you are
> >> using, so it could be a great resource to others who are ramping up to do
> >> similar things.
> >>
> >>   What I would like to keep doing is setup a new page for each FlyBase
> >>> data class that has a mapping table.  I tried putting them all into one page
> >>> but I started to get warning messages about editing large pages from
> >>> wikimedia.
> >>>
> >>
> >> I wouldn't worry about the warning message unless you are on a slow and/or
> >> spotty internet connection or some kind of ancient browser. I've had no
> >> problem whatsoever editing pages that vastly exceed the limit that seems to
> >> trigger this.
> >>
> >>    -hilmar
> >>
> >
>