Hi David, I loaded that database and tried it. I found that there is no primary key in the schema. That cause the problem that foreign key relations are missing.
Yong On 13/03/09 12:13 PM, "David Riley" <[email protected]> wrote: 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 <http://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> >> <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 <http://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 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.
