Hi Adam, this was a tough one but have some good news for you :) It appears that the addition of column "prepkit_key_1022" confuses MConfigurator due to 'key' in its name. This not a mistake on your part but an omission on our part. We need to ask MConfigurator to ignore such names.
For now I suggest you change this name not to contain 'key' in the middle. I dropped this column from both of your main tables, created new config and was able to query library dm without an exception. Hopefully this should fix it. Please let us know if you have any more problems, a On Tue, Aug 7, 2012 at 3:42 PM, Adam Wright <[email protected]> wrote: > Hi Arek, > > The previous schema you were looking at is what I used as a source > database for creating the mart with the XML file that I sent you. None of > the tables were created with BioMart in the source database. Unfortunately, > I do not have a copy of the resulting mart database from the XML file that > I have previously attached. I am currently using the same source database > but have changed a couple of things since I have sent the last XML file. > Although, I am still getting the same problem not being able to search the > dimension tables. > > I have attached a copy of the XML file that, I believe, I used to create > the resulting pancure_mart data-set. > > Hopefully this helps... If you need anything else let me know! > > Thanks for taking a look, > Adam Wright > Bioinformatics Software Developer > 647-260-6479 > > Ontario Institute for Cancer Research > MaRS Centre, South Tower > 101 College Street, Suite 800 > Toronto, Ontario, Canada M5G 0A3 > > 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. > ________________________________________ > From: Arek Kasprzyk [[email protected]] > Sent: 07 August 2012 05:59 > To: Adam Wright > Subject: Re: [BioMart Users] FW: Dataset not found > > Hi Adam, > thanks for the schema. I am not sure which of the 31 tables that you sent > me were generated by MBuilder? > > > cheers, > a > > On Fri, Aug 3, 2012 at 2:18 PM, Adam Wright <[email protected] > <mailto:[email protected]>> wrote: > Hi Arek, > > I have attached both the mySQL schema and the XML file from MartBuilder. > > Adam Wright > Bioinformatics Software Developer > 647-260-6479 > > Ontario Institute for Cancer Research > MaRS Centre, South Tower > 101 College Street, Suite 800 > Toronto, Ontario, Canada M5G 0A3 > > 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. > ________________________________ > From: Arek Kasprzyk [[email protected]<mailto: > [email protected]>] > Sent: 03 August 2012 05:55 > To: Adam Wright > Cc: [email protected]<mailto:[email protected]> > Subject: Re: [BioMart Users] FW: Dataset not found > > Hi Adam, > could you send me your MySQL schema so that i can reproduce the problem > here? > > a > > > On Fri, Aug 3, 2012 at 1:18 AM, Adam Wright <[email protected] > <mailto:[email protected]>> wrote: > Hi BioMart Users, > > > I am trying to create a BioMart instance and have run into an error that I > would appreciate help diagnosing. > > I set up the mart with MartBuilder 0.7 and am trying to run the > configuration and website with BioMart 0.8. Just as a side note, I am using > MartBuilder 0.7 instead of 0.8 because I am needing to manage the relations > between tables and other features that I wasn't able to do with version > 0.8. I am not sure what is going wrong exactly but, I am getting an error > when trying to query attributes from a dimension table through the web > interface. I have attached the error log for this. Also when I try to use > mart editor 0.7 it gives the error that the data-sets do not exist. Also it > appears as if both MartConfigurator and MartEditor are aware of the > relations all of the relationships. > > I have everything setup on my local machine. I am using mySQL and > connecting with a user that has full privileges to the databases on the > mySQL server. > > Please let me know if there is anything I am missing or if you need any > more information. Help would be greatly appreciated. > > Regards, > Adam Wright > Bioinformatics Software Developer > 647-260-6479 > > Ontario Institute for Cancer Research > MaRS Centre, South Tower > 101 College Street, Suite 800 > Toronto, Ontario, Canada M5G 0A3 > > 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. > ________________________________ > From: Joachim Baran > Sent: 02 August 2012 16:34 > To: Adam Wright > Subject: Exception. > > > > > Joachim Baran, PhD > Database/Application Programmer, Informatics and Bio-computing > > Ontario Institute for Cancer Research > MaRS Centre, South Tower > 101 College Street, Suite 800 > Toronto, Ontario, Canada M5G 0A3 > > Tel: 647-258-4319 > 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. > > > > > > _______________________________________________ > Users mailing list > [email protected]<mailto:[email protected]> > https://lists.biomart.org/mailman/listinfo/users > > > > > -- > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead > www.biomart.org<http://www.biomart.org> > >
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