On Fri, 2007-12-07 at 12:22 +0000, Michael Wicks wrote:
> Arek, Syed and Steffen - Many thanks for your comments and advice.
>
> I now understand the configure.pl issue and will investigate the
> exportables problem by looking at your suggested examples.
>
> The Refresh Problem I was referring to was of the data in the Mart
> itself, NOT what the Mart consists of structurally. For us, rebuilding
> the Mart manually everyday is not a viable option - life is too short,
> and my boss would like me to do some other work, I'm sure :-)
>
> What has occurred to me after reading your suggestions, is the fact that
> I have captured the SQL generated by MartBuilder as a text file (as well
> as invoking MartRunner), when I created our Mart. Therefore it would
> seem to me an easy option to take this SQL, amend it to refresh, not
> create, all the components in my Mart, by running this amended SQL as a
> Cron job, for example. Does this seem like a good course of action to
> you? Are there any pitfalls that I need to avoid? (Other than the
> usual pitfalls of editing a large set of SQL commands!)
As long as you understand which bits of data you are moving across, its
fine. a script invoked by crontab is the right way to go.
>
> (Also I am aware that the presentational components of any Mart, as
> maintained via MartEditor, are stored in the Mart itself, so I would
> have to be careful that I didn't remove these in my update SQL script.
> I don't know the internal structure of Marts, but can I assume that the
> SQL generated by MartBuilder doesn't affect any components that
> MartEditor creates/updates?)
>
The tables MartEditor owns and fiddle with are like "meta%" in the mart.
> Suggestion for future development: it would be great if MartEditor had a
> command line alternative, so I could store my presentational XML
> somewhere and apply it via a shell script for example. Also, it would
> be great if the SQL generated by MartBuilder could be flexible enough to
> be re-runnable, thus solving my problem ("Drop Table If Exists....." in
> MySQL, for example).
You can use SaveAll option to dump the XMLs. modification is dangerous
unless you are 100% sure about what you are doing. If your requirement
is only exporting XML from command line with out editing, then where do
you intend to get the XML in the first place. The helper tools are there
not only to assist but to safe guard the system from serious accidents
which may harm data in the database.
For MartBuilder, Richard would be able to guide you through.
hope this helps.
cheers
syed
>
> Anyway, thanks for your help once again
>
> Mike Wicks
>
>
>
>
> Arek Kasprzyk wrote:
> >
> > On 7 Dec 2007, at 11:22, sneumann wrote:
> >
> >> On Fr, 2007-12-07 at 10:38 +0000, Arek Kasprzyk wrote:
> >> ...
> >>> If you just mean 'data in the db changes' then as I said
> >>> previously you drop your mart and you re-run mart build again (using
> >> If you have enough space in your db,
> >> you would import into a new mysql database,
> >> stop your mart applications, rename new to current
> >> and restart. This minimizes downtime.
> >
> > Hi Steffen,
> > yes this is exactly how we do it :)
> >
> > a.
> >
> >
> >>
> >> Yours,
> >> Steffen
> >>
> >> -- IPB Halle AG Massenspektrometrie & Bioinformatik
> >> Dr. Steffen Neumann http://www.IPB-Halle.DE
> >> Weinberg 3 http://msbi.bic-gh.de
> >> 06120 Halle Tel. +49 (0) 345 5582 - 1470
> >> +49 (0) 345 5582 - 0
> >> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
> >>
> >>
> >
> >
> > -------------------------------------------------------------------------------
> >
> > Arek Kasprzyk
> > EMBL-European Bioinformatics Institute.
> > Wellcome Trust Genome Campus, Hinxton,
> > Cambridge CB10 1SD, UK.
> > Tel: +44-(0)1223-494606
> > Fax: +44-(0)1223-494468
> > -------------------------------------------------------------------------------
> >
> >
> >
> >
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
