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. > >
