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[BioMart Users] FW: Dataset not found

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Adam Wright

[BioMart Users] FW: Dataset not found

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

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

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
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

exception.txt (18K) Download Attachment

Arek Kasprzyk

Re: [BioMart Users] FW: Dataset not found

Hi Adam,

could you send me your MySQL schema so that i can reproduce the problem here?

On Fri, Aug 3, 2012 at 1:18 AM, Adam Wright <[hidden email]> 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

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

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
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

Adam Wright

Re: [BioMart Users] FW: Dataset not found

Hi Arek,

I have attached both the mySQL schema and the XML file from MartBuilder.

From: Arek Kasprzyk [[hidden email]]
Sent: 03 August 2012 05:55
To: Adam Wright
Cc: [hidden email]
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?

On Fri, Aug 3, 2012 at 1:18 AM, Adam Wright <[hidden email]> 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

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

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
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

pancure_test.xml (75K) Download Attachment

biomart_source.sql (38K) Download Attachment

Joachim Baran-3

Re: [BioMart Users] FW: Dataset not found

Hello,

It appears that the relationship between the tables 'donor' and 'library' is not good, in the sense that making 'library' a sub-class of 'donor' breaks the mart. In MartBuilder, a red-line is drawn between 'donor' and its sub-class 'library', but I could not find out what that concretely means.

A workaround I found involves merging 'library' and 'donor', which then directly exposes tables linked to 'library' as dimension tables of 'donor'.

Whilst that the workaround provides a functioning mart, I am wondering whether there is a better solution to the problem. Any suggestions?

Thanks,

Joachim

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

Arek Kasprzyk

Re: [BioMart Users] FW: Dataset not found

In reply to this post by Adam Wright

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,

On Tue, Aug 7, 2012 at 3:42 PM, Adam Wright <[hidden email]> 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 [[hidden email]]
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 <[hidden email]<mailto:[hidden email]>> 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 [[hidden email]<mailto:[hidden email]>]

Sent: 03 August 2012 05:55
To: Adam Wright

Cc: [hidden email]<mailto:[hidden email]>

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 <[hidden email]<mailto:[hidden email]>> 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

[hidden email]<mailto:[hidden email]>

https://lists.biomart.org/mailman/listinfo/users

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead

www.biomart.org<http://www.biomart.org>

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

Adam Wright

Re: [BioMart Users] FW: Dataset not found

Thanks Arek,

I am very Glad you figured this out. I will definitely make this change tomorrow. I will add the rest of the tables back into the mart and will let you know how it goes. I am excited to see it all working!!!

I greatly appreciate your help!!!

Thanks and 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

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 [[hidden email]]
Sent: 08 August 2012 13:12
To: Adam Wright
Cc: [hidden email]
Subject: Re: [BioMart Users] FW: Dataset not found

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 <[hidden email]<mailto:[hidden email]>> 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<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 [[hidden email]<mailto:[hidden email]>]
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 <[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> 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><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 [[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>]
Sent: 03 August 2012 05:55
To: Adam Wright
Cc: [hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>
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 <[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> 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><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><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
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>
https://lists.biomart.org/mailman/listinfo/users

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org<http://www.biomart.org><http://www.biomart.org>

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users