Hi Scott,
Sure does. As an example, here is featureloc (just the foreign key section
of \d):
Foreign-key constraints:
"fk_featureloc01" FOREIGN KEY (feature_id) REFERENCES
feature(feature_id)
"fk_featureloc02" FOREIGN KEY (srcfeature_id) REFERENCES
feature(feature_id)
On Fri, Mar 13, 2009 at 12:07 PM, Scott Cain <[email protected]> wrote:
> Hi Dave,
>
> I haven't loaded up that database, but does \d <tablename> report
> foreign key constraints properly? I wonder if there is a problem with
> the schema in that dump.
>
> Scott
>
>
> On Fri, Mar 13, 2009 at 11:43 AM, David Riley
> <[email protected]> wrote:
> > Very interesting. I don't have a problem with that database either. Keys
> are
> > pulled without a problem. A postgres dump of the database I am trying to
> use
> > is here:
> >
> > http://downloads.sourceforge.net/sybil/strepneumo_v7.dump.gz
> >
> > I have tried with a database loaded into postgres 8.1.9 and 8.2.5 with
> the
> > same results. I don't have a publicly available one but I am testing
> using
> > the data from this dump.
> >
> > Thanks so much for the quick replies.
> >
> > Dave
> >
> > On Fri, Mar 13, 2009 at 10:02 AM, Yong Liang <[email protected]>
> wrote:
> >>
> >> Hi David,
> >>
> >> I tested Mbuilder on a public chado and didn’t find the foreign key
> >> problem.
> >>
> >> The public readonly chado is available at:
> >> Host: flybase.org ; port: 5432 ; database: flybase ; schema: public ;
> >> username: flybase ; password:
> >>
> >> If you could point us to where we could get this schema, we will check
> it
> >> for you.
> >>
> >> For the get first 10 rows problem, this is a bug of Mbuilder, I tried to
> >> get the first 10 rows from table analysisfeature and it kept running for
> 30
> >> minutes ... I had to manually stop it. The table has 21,791,848 rows.
> >>
> >> I checked the code, the implementation takes all the results first and
> >> then let you see the first 10. That causes the problem. We will look
> into
> >> it and get back to you soon.
> >>
> >> If you have any other problems, please let us know.
> >>
> >> Thanks,
> >>
> >>
> >>
> >>
> >> On 12/03/09 3:46 PM, "David Riley" <[email protected]>
> >> wrote:
> >>
> >> Hi all,
> >>
> >> I am very new to BioMart and my goal is to use it to build marts on a
> >> Chado instance for the Sybil package (sybil.sf.net <http://sybil.sf.net>
> ).
> >> My goal is to build a fairly comprehensive and easy to use search
> builder
> >> using extjs with BioMart driving the search data sets and filters. I'm
> just
> >> starting out but I have already run into a bit of a snag.
> >>
> >> I am trying to connect Martbuilder 0.7 to a Postgres 8.1 Chado instance.
> >> All the tables seem to get pulled down properly but non of the foreign
> key
> >> relationships or unique key constraints. The keyguessing mechanism works
> >> alright except there are several instances where a table has a type_id
> >> column that needs to be linked to a cvterm_id column and these are lost
> and
> >> kind of integral to the schema.
> >>
> >> I am wondering if anyone is currently using BioMart with a Chado
> instance
> >> and if so how.
> >>
> >> I have also noticed that even doing the 'give me the first 10 rows'
> causes
> >> an OutOfMemory exception. The database I am trying to connect to has
> >> 7,607,708 rows in feature and I am wondering if this is a bit bigger
> than
> >> BioMart was designed for.
> >>
> >> I noticed some warnings about Java 1.6 which happens to be the version I
> >> am using so this may explain the memory problem.
> >>
> >> Any help and/or Chado BioMart experiences would be greatly appreciated.
> >>
> >> Thanks,
> >>
> >> Dave
> >>
> >>
> >> Yong Liang
> >> Database/Application Programmer
> >>
> >> Ontario Institute for Cancer Research
> >> MaRS Centre, South Tower
> >> 101 College Street, Suite 800
> >> Toronto, Ontario, Canada M5G 0A3
> >>
> >> Tel: 647-260-7951
> >> Toll-free: 1-866-678-6427
> >> www.oicr.on.ca
> >>
> >> This message and any attachments may contain confidential and/or
> >> privileged information for the sole use of the intended recipient. Any
> >> review or distribution by anyone other than the person for whom it was
> >> originally intended is strictly prohibited. If you have received this
> >> message in error, please contact the sender and delete all copies.
> Opinions,
> >> conclusions or other information contained in this message may not be
> that
> >> of the organization.
> >>
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D. scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/) 216-392-3087
> Ontario Institute for Cancer Research
>
