[BioMart Users] biomart v0.8 : error creating mart from Chado schema

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[BioMart Users] biomart v0.8 : error creating mart from Chado schema

Aminah Keliet
Hi

We are testing the new version of Biomart (0.8 rc 6) to replace our
current install (v 0.7). We build mart on the GMOD-Chado schema using
the feature table as main table for our marts. With the new version we
get an error when we try to do the same thing. In the Add data source
panel, we choose the feature table from the public schema, then we click
add and we get :

[AWT-EventQueue-1] INFO martconfigurator - Done saving settings
[Thread-104] INFO martconfigurator - Initialize source schema
[Thread-104] INFO martconfigurator - Done synchronising
[Thread-104] ERROR martconfigurator - duplicated relation
feature.[feature_id_1057] -> feature__feature_genotype.[feature_id_1057]
[AWT-EventQueue-1] ERROR martconfigurator - Exception occurred in
MartBuilder
org.biomart.common.exceptions.BioMartError:
org.biomart.common.exceptions.AssociationException: A relation between
these two keys already exists.
    at
org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:231)
    at
org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:369)
    at
org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:484)
    at
org.biomart.configurator.controller.MartController.synchronise(MartController.java:900)
    at
org.biomart.configurator.controller.MartController.suggestMarts(MartController.java:1375)
    at
org.biomart.configurator.controller.MartController.requestCreateMartsFromSource(MartController.java:1599)
    at
org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:98)
    at
org.biomart.configurator.view.component.container.SourceGroupPanel$1.construct(SourceGroupPanel.java:85)
    at org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128)
    at java.lang.Thread.run(Thread.java:619)
Caused by: org.biomart.common.exceptions.AssociationException: A
relation between these two keys already exists.
    at org.biomart.objects.objects.Relation.<init>(Relation.java:141)
    at
org.biomart.objects.objects.RelationTarget.<init>(RelationTarget.java:17)
    at
org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:225)
    ... 9 more

Do you have any idea ?
Thanks

--
Aminah Olivia KELIET
Ingenieur d'études en Bio-informatique

Unité de recherche en Génomique-Info
INRA Centre de Versailles
Route de Saint Cyr
78026 Versailles Cedex

email: [hidden email]
url:http://urgi.versailles.inra.fr
tel: 01.30.83.37.74

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Re: [BioMart Users] biomart v0.8 : error creating mart from Chado schema

Junjun Zhang
Hi Aminah,

Is that chado schema publicly available? It would be very helpful if we can test it out here.

Also, I am just curious how your current mart is built. If you'd like to try 0.8 with the existing mart db, you can directly import it using martconfigurator.

Best regards,

Junjun
Sent from my BBerry

----- Original Message -----
From: Aminah Keliet [mailto:[hidden email]]
Sent: Tuesday, July 26, 2011 10:34 AM
To: [hidden email] <[hidden email]>
Subject: [BioMart Users] biomart v0.8 : error creating mart from Chado schema

Hi

We are testing the new version of Biomart (0.8 rc 6) to replace our
current install (v 0.7). We build mart on the GMOD-Chado schema using
the feature table as main table for our marts. With the new version we
get an error when we try to do the same thing. In the Add data source
panel, we choose the feature table from the public schema, then we click
add and we get :

[AWT-EventQueue-1] INFO martconfigurator - Done saving settings
[Thread-104] INFO martconfigurator - Initialize source schema
[Thread-104] INFO martconfigurator - Done synchronising
[Thread-104] ERROR martconfigurator - duplicated relation
feature.[feature_id_1057] -> feature__feature_genotype.[feature_id_1057]
[AWT-EventQueue-1] ERROR martconfigurator - Exception occurred in
MartBuilder
org.biomart.common.exceptions.BioMartError:
org.biomart.common.exceptions.AssociationException: A relation between
these two keys already exists.
    at
org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:231)
    at
org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:369)
    at
org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:484)
    at
org.biomart.configurator.controller.MartController.synchronise(MartController.java:900)
    at
org.biomart.configurator.controller.MartController.suggestMarts(MartController.java:1375)
    at
org.biomart.configurator.controller.MartController.requestCreateMartsFromSource(MartController.java:1599)
    at
org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:98)
    at
org.biomart.configurator.view.component.container.SourceGroupPanel$1.construct(SourceGroupPanel.java:85)
    at org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128)
    at java.lang.Thread.run(Thread.java:619)
Caused by: org.biomart.common.exceptions.AssociationException: A
relation between these two keys already exists.
    at org.biomart.objects.objects.Relation.<init>(Relation.java:141)
    at
org.biomart.objects.objects.RelationTarget.<init>(RelationTarget.java:17)
    at
org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:225)
    ... 9 more

Do you have any idea ?
Thanks

--
Aminah Olivia KELIET
Ingenieur d'études en Bio-informatique

Unité de recherche en Génomique-Info
INRA Centre de Versailles
Route de Saint Cyr
78026 Versailles Cedex

email: [hidden email]
url:http://urgi.versailles.inra.fr
tel: 01.30.83.37.74

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] biomart v0.8 : error creating mart from Chado schema

Aminah Keliet
Hi,

Yes, we use a chado schema postgres publicly available.
The current mart was built easily with martbuilder (martbuiler.sh). We
have chosen the feature table as main table without problems, and it
works well.

I'll try to directly import existing marts with martconfigurator. I'll
keep you informed.

Then, with this new release of Biomart (0.8 rc 6), we can't create new
mart from Chado schema, using the table feature as a main table?


Best regards,


Aminah,


Junjun Zhang wrote:

> Hi Aminah,
>
> Is that chado schema publicly available? It would be very helpful if we can test it out here.
>
> Also, I am just curious how your current mart is built. If you'd like to try 0.8 with the existing mart db, you can directly import it using martconfigurator.
>
> Best regards,
>
> Junjun
> Sent from my BBerry
>
> ----- Original Message -----
> From: Aminah Keliet [mailto:[hidden email]]
> Sent: Tuesday, July 26, 2011 10:34 AM
> To: [hidden email] <[hidden email]>
> Subject: [BioMart Users] biomart v0.8 : error creating mart from Chado schema
>
> Hi
>
> We are testing the new version of Biomart (0.8 rc 6) to replace our
> current install (v 0.7). We build mart on the GMOD-Chado schema using
> the feature table as main table for our marts. With the new version we
> get an error when we try to do the same thing. In the Add data source
> panel, we choose the feature table from the public schema, then we click
> add and we get :
>
> [AWT-EventQueue-1] INFO martconfigurator - Done saving settings
> [Thread-104] INFO martconfigurator - Initialize source schema
> [Thread-104] INFO martconfigurator - Done synchronising
> [Thread-104] ERROR martconfigurator - duplicated relation
> feature.[feature_id_1057] -> feature__feature_genotype.[feature_id_1057]
> [AWT-EventQueue-1] ERROR martconfigurator - Exception occurred in
> MartBuilder
> org.biomart.common.exceptions.BioMartError:
> org.biomart.common.exceptions.AssociationException: A relation between
> these two keys already exists.
>     at
> org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:231)
>     at
> org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:369)
>     at
> org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:484)
>     at
> org.biomart.configurator.controller.MartController.synchronise(MartController.java:900)
>     at
> org.biomart.configurator.controller.MartController.suggestMarts(MartController.java:1375)
>     at
> org.biomart.configurator.controller.MartController.requestCreateMartsFromSource(MartController.java:1599)
>     at
> org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:98)
>     at
> org.biomart.configurator.view.component.container.SourceGroupPanel$1.construct(SourceGroupPanel.java:85)
>     at org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128)
>     at java.lang.Thread.run(Thread.java:619)
> Caused by: org.biomart.common.exceptions.AssociationException: A
> relation between these two keys already exists.
>     at org.biomart.objects.objects.Relation.<init>(Relation.java:141)
>     at
> org.biomart.objects.objects.RelationTarget.<init>(RelationTarget.java:17)
>     at
> org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:225)
>     ... 9 more
>
> Do you have any idea ?
> Thanks
>
>  
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Re: [BioMart Users] biomart v0.8 : error creating mart from Chado schema

Lincoln Stein
In reply to this post by Junjun Zhang

Hi Junjun,

I'm bringing Scott Cain into this conversation as he supports the Chado schema for GMOD.

Lincoln

On Tuesday, July 26, 2011, Junjun Zhang <[hidden email]> wrote:
> Hi Aminah,
>
> Is that chado schema publicly available? It would be very helpful if we can test it out here.
>
> Also, I am just curious how your current mart is built. If you'd like to try 0.8 with the existing mart db, you can directly import it using martconfigurator.
>
> Best regards,
>
> Junjun
> Sent from my BBerry
>
> ----- Original Message -----
> From: Aminah Keliet [mailto:[hidden email]]
> Sent: Tuesday, July 26, 2011 10:34 AM
> To: [hidden email] <[hidden email]>
> Subject: [BioMart Users] biomart v0.8 : error creating mart from Chado schema
>
> Hi
>
> We are testing the new version of Biomart (0.8 rc 6) to replace our
> current install (v 0.7). We build mart on the GMOD-Chado schema using
> the feature table as main table for our marts. With the new version we
> get an error when we try to do the same thing. In the Add data source
> panel, we choose the feature table from the public schema, then we click
> add and we get :
>
> [AWT-EventQueue-1] INFO martconfigurator - Done saving settings
> [Thread-104] INFO martconfigurator - Initialize source schema
> [Thread-104] INFO martconfigurator - Done synchronising
> [Thread-104] ERROR martconfigurator - duplicated relation
> feature.[feature_id_1057] -> feature__feature_genotype.[feature_id_1057]
> [AWT-EventQueue-1] ERROR martconfigurator - Exception occurred in
> MartBuilder
> org.biomart.common.exceptions.BioMartError:
> org.biomart.common.exceptions.AssociationException: A relation between
> these two keys already exists.
>    at
> org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:231)
>    at
> org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:369)
>    at
> org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:484)
>    at
> org.biomart.configurator.controller.MartController.synchronise(MartController.java:900)
>    at
> org.biomart.configurator.controller.MartController.suggestMarts(MartController.java:1375)
>    at
> org.biomart.configurator.controller.MartController.requestCreateMartsFromSource(MartController.java:1599)
>    at
> org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:98)
>    at
> org.biomart.configurator.view.component.container.SourceGroupPanel$1.construct(SourceGroupPanel.java:85)
>    at org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128)
>    at java.lang.Thread.run(Thread.java:619)
> Caused by: org.biomart.common.exceptions.AssociationException: A
> relation between these two keys already exists.
>    at org.biomart.objects.objects.Relation.<init>(Relation.java:141)
>    at
> org.biomart.objects.objects.RelationTarget.<init>(RelationTarget.java:17)
>    at
> org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:225)
>    ... 9 more
>
> Do you have any idea ?
> Thanks
>
> --
> Aminah Olivia KELIET
> Ingenieur d'études en Bio-informatique
>
> Unité de recherche en Génomique-Info
> INRA Centre de Versailles
> Route de Saint Cyr
> 78026 Versailles Cedex
>
> email: [hidden email]
> url:http://urgi.versailles.inra.fr
> tel: 01.30.83.37.74
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: [BioMart Users] biomart v0.8 : error creating mart from Chado schema

Junjun Zhang
In reply to this post by Aminah Keliet
Hi Aminah,

It is the plan to incorporate MartBuilder's features into
MartConfigurator. However, at this time this is a low priority,
MartConfigurator currently only supports very basic MartBuilder features,
and it has not been properly tested. So it's not recommended to use
MartConfigurator to transform source schema to BioMart schema yet.

Please feel free to let us know if you have any further questions.

Thanks,
Junjun



On 11-07-27 3:51 AM, "Aminah Keliet"
<[hidden email]> wrote:

>Hi,
>
>Yes, we use a chado schema postgres publicly available.
>The current mart was built easily with martbuilder (martbuiler.sh). We
>have chosen the feature table as main table without problems, and it
>works well.
>
>I'll try to directly import existing marts with martconfigurator. I'll
>keep you informed.
>
>Then, with this new release of Biomart (0.8 rc 6), we can't create new
>mart from Chado schema, using the table feature as a main table?
>
>
>Best regards,
>
>
>Aminah,
>
>
>Junjun Zhang wrote:
>> Hi Aminah,
>>
>> Is that chado schema publicly available? It would be very helpful if we
>>can test it out here.
>>
>> Also, I am just curious how your current mart is built. If you'd like
>>to try 0.8 with the existing mart db, you can directly import it using
>>martconfigurator.
>>
>> Best regards,
>>
>> Junjun
>> Sent from my BBerry
>>
>> ----- Original Message -----
>> From: Aminah Keliet [mailto:[hidden email]]
>> Sent: Tuesday, July 26, 2011 10:34 AM
>> To: [hidden email] <[hidden email]>
>> Subject: [BioMart Users] biomart v0.8 : error creating mart from Chado
>>schema
>>
>> Hi
>>
>> We are testing the new version of Biomart (0.8 rc 6) to replace our
>> current install (v 0.7). We build mart on the GMOD-Chado schema using
>> the feature table as main table for our marts. With the new version we
>> get an error when we try to do the same thing. In the Add data source
>> panel, we choose the feature table from the public schema, then we
>>click
>> add and we get :
>>
>> [AWT-EventQueue-1] INFO martconfigurator - Done saving settings
>> [Thread-104] INFO martconfigurator - Initialize source schema
>> [Thread-104] INFO martconfigurator - Done synchronising
>> [Thread-104] ERROR martconfigurator - duplicated relation
>> feature.[feature_id_1057] -> feature__feature_genotype.[feature_id_1057]
>> [AWT-EventQueue-1] ERROR martconfigurator - Exception occurred in
>> MartBuilder
>> org.biomart.common.exceptions.BioMartError:
>> org.biomart.common.exceptions.AssociationException: A relation between
>> these two keys already exists.
>>     at
>>
>>org.biomart.configurator.controller.MartController.processParentDatasetTa
>>ble(MartController.java:231)
>>     at
>>
>>org.biomart.configurator.controller.MartController.generateDatasetTable(M
>>artController.java:369)
>>     at
>>
>>org.biomart.configurator.controller.MartController.generateDatasetTable(M
>>artController.java:484)
>>     at
>>
>>org.biomart.configurator.controller.MartController.synchronise(MartContro
>>ller.java:900)
>>     at
>>
>>org.biomart.configurator.controller.MartController.suggestMarts(MartContr
>>oller.java:1375)
>>     at
>>
>>org.biomart.configurator.controller.MartController.requestCreateMartsFrom
>>Source(MartController.java:1599)
>>     at
>>
>>org.biomart.configurator.controller.ObjectController.initMarts(ObjectCont
>>roller.java:98)
>>     at
>>
>>org.biomart.configurator.view.component.container.SourceGroupPanel$1.cons
>>truct(SourceGroupPanel.java:85)
>>     at
>>org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128)
>>     at java.lang.Thread.run(Thread.java:619)
>> Caused by: org.biomart.common.exceptions.AssociationException: A
>> relation between these two keys already exists.
>>     at org.biomart.objects.objects.Relation.<init>(Relation.java:141)
>>     at
>>
>>org.biomart.objects.objects.RelationTarget.<init>(RelationTarget.java:17)
>>     at
>>
>>org.biomart.configurator.controller.MartController.processParentDatasetTa
>>ble(MartController.java:225)
>>     ... 9 more
>>
>> Do you have any idea ?
>> Thanks
>>
>>  

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Re: [BioMart Users] biomart v0.8 : error creating mart from Chado schema

Junjun Zhang
In reply to this post by Lincoln Stein
Sure, thanks Lincoln!

Scott, can you please recommend any publicly available chado db dump so that we can load locally for testing BioMart data transformation?

Thanks,
Junjun


From: Lincoln Stein <[hidden email]>
Date: Wed, 27 Jul 2011 08:25:44 -0400
To: jzhang <[hidden email]>, Scott Cain <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: Re: [BioMart Users] biomart v0.8 : error creating mart from Chado schema


Hi Junjun,

I'm bringing Scott Cain into this conversation as he supports the Chado schema for GMOD.

Lincoln

On Tuesday, July 26, 2011, Junjun Zhang <[hidden email]> wrote:
> Hi Aminah,
>
> Is that chado schema publicly available? It would be very helpful if we can test it out here.
>
> Also, I am just curious how your current mart is built. If you'd like to try 0.8 with the existing mart db, you can directly import it using martconfigurator.
>
> Best regards,
>
> Junjun
> Sent from my BBerry
>
> ----- Original Message -----
> From: Aminah Keliet [mailto:[hidden email]]
> Sent: Tuesday, July 26, 2011 10:34 AM
> To: [hidden email] <[hidden email]>
> Subject: [BioMart Users] biomart v0.8 : error creating mart from Chado schema
>
> Hi
>
> We are testing the new version of Biomart (0.8 rc 6) to replace our
> current install (v 0.7). We build mart on the GMOD-Chado schema using
> the feature table as main table for our marts. With the new version we
> get an error when we try to do the same thing. In the Add data source
> panel, we choose the feature table from the public schema, then we click
> add and we get :
>
> [AWT-EventQueue-1] INFO martconfigurator - Done saving settings
> [Thread-104] INFO martconfigurator - Initialize source schema
> [Thread-104] INFO martconfigurator - Done synchronising
> [Thread-104] ERROR martconfigurator - duplicated relation
> feature.[feature_id_1057] -> feature__feature_genotype.[feature_id_1057]
> [AWT-EventQueue-1] ERROR martconfigurator - Exception occurred in
> MartBuilder
> org.biomart.common.exceptions.BioMartError:
> org.biomart.common.exceptions.AssociationException: A relation between
> these two keys already exists.
>    at
> org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:231)
>    at
> org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:369)
>    at
> org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:484)
>    at
> org.biomart.configurator.controller.MartController.synchronise(MartController.java:900)
>    at
> org.biomart.configurator.controller.MartController.suggestMarts(MartController.java:1375)
>    at
> org.biomart.configurator.controller.MartController.requestCreateMartsFromSource(MartController.java:1599)
>    at
> org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:98)
>    at
> org.biomart.configurator.view.component.container.SourceGroupPanel$1.construct(SourceGroupPanel.java:85)
>    at org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128)
>    at java.lang.Thread.run(Thread.java:619)
> Caused by: org.biomart.common.exceptions.AssociationException: A
> relation between these two keys already exists.
>    at org.biomart.objects.objects.Relation.<init>(Relation.java:141)
>    at
> org.biomart.objects.objects.RelationTarget.<init>(RelationTarget.java:17)
>    at
> org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:225)
>    ... 9 more
>
> Do you have any idea ?
> Thanks
>
> --
> Aminah Olivia KELIET
> Ingenieur d'études en Bio-informatique
>
> Unité de recherche en Génomique-Info
> INRA Centre de Versailles
> Route de Saint Cyr
> 78026 Versailles Cedex
>
> email: [hidden email]
> url:http://urgi.versailles.inra.fr
> tel: 01.30.83.37.74
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: [BioMart Users] biomart v0.8 : error creating mart from Chado schema

Scott Cain
In reply to this post by Lincoln Stein
Hi All,

Thanks for bringing me into the conversation; please let me know if
there is anything I can do to help.

Scott


On Wed, Jul 27, 2011 at 8:25 AM, Lincoln Stein <[hidden email]> wrote:

>
> Hi Junjun,
>
> I'm bringing Scott Cain into this conversation as he supports the Chado
> schema for GMOD.
>
> Lincoln
>
> On Tuesday, July 26, 2011, Junjun Zhang <[hidden email]> wrote:
>> Hi Aminah,
>>
>> Is that chado schema publicly available? It would be very helpful if we
>> can test it out here.
>>
>> Also, I am just curious how your current mart is built. If you'd like to
>> try 0.8 with the existing mart db, you can directly import it using
>> martconfigurator.
>>
>> Best regards,
>>
>> Junjun
>> Sent from my BBerry
>>
>> ----- Original Message -----
>> From: Aminah Keliet [mailto:[hidden email]]
>> Sent: Tuesday, July 26, 2011 10:34 AM
>> To: [hidden email] <[hidden email]>
>> Subject: [BioMart Users] biomart v0.8 : error creating mart from Chado
>> schema
>>
>> Hi
>>
>> We are testing the new version of Biomart (0.8 rc 6) to replace our
>> current install (v 0.7). We build mart on the GMOD-Chado schema using
>> the feature table as main table for our marts. With the new version we
>> get an error when we try to do the same thing. In the Add data source
>> panel, we choose the feature table from the public schema, then we click
>> add and we get :
>>
>> [AWT-EventQueue-1] INFO martconfigurator - Done saving settings
>> [Thread-104] INFO martconfigurator - Initialize source schema
>> [Thread-104] INFO martconfigurator - Done synchronising
>> [Thread-104] ERROR martconfigurator - duplicated relation
>> feature.[feature_id_1057] -> feature__feature_genotype.[feature_id_1057]
>> [AWT-EventQueue-1] ERROR martconfigurator - Exception occurred in
>> MartBuilder
>> org.biomart.common.exceptions.BioMartError:
>> org.biomart.common.exceptions.AssociationException: A relation between
>> these two keys already exists.
>>    at
>>
>> org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:231)
>>    at
>>
>> org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:369)
>>    at
>>
>> org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:484)
>>    at
>>
>> org.biomart.configurator.controller.MartController.synchronise(MartController.java:900)
>>    at
>>
>> org.biomart.configurator.controller.MartController.suggestMarts(MartController.java:1375)
>>    at
>>
>> org.biomart.configurator.controller.MartController.requestCreateMartsFromSource(MartController.java:1599)
>>    at
>>
>> org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:98)
>>    at
>>
>> org.biomart.configurator.view.component.container.SourceGroupPanel$1.construct(SourceGroupPanel.java:85)
>>    at org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128)
>>    at java.lang.Thread.run(Thread.java:619)
>> Caused by: org.biomart.common.exceptions.AssociationException: A
>> relation between these two keys already exists.
>>    at org.biomart.objects.objects.Relation.<init>(Relation.java:141)
>>    at
>> org.biomart.objects.objects.RelationTarget.<init>(RelationTarget.java:17)
>>    at
>>
>> org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:225)
>>    ... 9 more
>>
>> Do you have any idea ?
>> Thanks
>>
>> --
>> Aminah Olivia KELIET
>> Ingenieur d'études en Bio-informatique
>>
>> Unité de recherche en Génomique-Info
>> INRA Centre de Versailles
>> Route de Saint Cyr
>> 78026 Versailles Cedex
>>
>> email: [hidden email]
>> url:http://urgi.versailles.inra.fr
>> tel: 01.30.83.37.74
>>
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
>>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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Re: [BioMart Users] biomart v0.8 : error creating mart from Chado schema

Arek Kasprzyk
In reply to this post by Junjun Zhang
Junjun:
chado schema is publically available and i have done quite a bit of
work with it in the past.
The end result was that MBuilder could support 3NF transformation
quite well but this was not sufficient for chado.
Chado is a schema with a lot of recursive self-referencing based
around 'feature' table. This, of course, can still be transformed
using 3NF algorithm but the end result will not be as exiciting as one
would like to. I experimented with it a bit a few years ago and came
up with an alternative to 3NF algorihm which would work much better
with chado. However given that current MConfigurator has not even
acquired all the MBuilder features this seems to be a long way ahead.
It will be better if you concentrate on implementing basic features
for MConfigurator to get 3NF going properly first. This will give you
the basics for chado. Once this is sorted out I"ll be glad to help
with a proper algorithm for chado transformation


a



On Tue, Jul 26, 2011 at 12:01 PM, Junjun Zhang <[hidden email]> wrote:

> Hi Aminah,
>
> Is that chado schema publicly available? It would be very helpful if we can test it out here.
>
> Also, I am just curious how your current mart is built. If you'd like to try 0.8 with the existing mart db, you can directly import it using martconfigurator.
>
> Best regards,
>
> Junjun
> Sent from my BBerry
>
> ----- Original Message -----
> From: Aminah Keliet [mailto:[hidden email]]
> Sent: Tuesday, July 26, 2011 10:34 AM
> To: [hidden email] <[hidden email]>
> Subject: [BioMart Users] biomart v0.8 : error creating mart from Chado schema
>
> Hi
>
> We are testing the new version of Biomart (0.8 rc 6) to replace our
> current install (v 0.7). We build mart on the GMOD-Chado schema using
> the feature table as main table for our marts. With the new version we
> get an error when we try to do the same thing. In the Add data source
> panel, we choose the feature table from the public schema, then we click
> add and we get :
>
> [AWT-EventQueue-1] INFO martconfigurator - Done saving settings
> [Thread-104] INFO martconfigurator - Initialize source schema
> [Thread-104] INFO martconfigurator - Done synchronising
> [Thread-104] ERROR martconfigurator - duplicated relation
> feature.[feature_id_1057] -> feature__feature_genotype.[feature_id_1057]
> [AWT-EventQueue-1] ERROR martconfigurator - Exception occurred in
> MartBuilder
> org.biomart.common.exceptions.BioMartError:
> org.biomart.common.exceptions.AssociationException: A relation between
> these two keys already exists.
>    at
> org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:231)
>    at
> org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:369)
>    at
> org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:484)
>    at
> org.biomart.configurator.controller.MartController.synchronise(MartController.java:900)
>    at
> org.biomart.configurator.controller.MartController.suggestMarts(MartController.java:1375)
>    at
> org.biomart.configurator.controller.MartController.requestCreateMartsFromSource(MartController.java:1599)
>    at
> org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:98)
>    at
> org.biomart.configurator.view.component.container.SourceGroupPanel$1.construct(SourceGroupPanel.java:85)
>    at org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128)
>    at java.lang.Thread.run(Thread.java:619)
> Caused by: org.biomart.common.exceptions.AssociationException: A
> relation between these two keys already exists.
>    at org.biomart.objects.objects.Relation.<init>(Relation.java:141)
>    at
> org.biomart.objects.objects.RelationTarget.<init>(RelationTarget.java:17)
>    at
> org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:225)
>    ... 9 more
>
> Do you have any idea ?
> Thanks
>
> --
> Aminah Olivia KELIET
> Ingenieur d'études en Bio-informatique
>
> Unité de recherche en Génomique-Info
> INRA Centre de Versailles
> Route de Saint Cyr
> 78026 Versailles Cedex
>
> email: [hidden email]
> url:http://urgi.versailles.inra.fr
> tel: 01.30.83.37.74
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
>
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Re: [BioMart Users] biomart v0.8 : error creating mart from Chado schema

Arek Kasprzyk
forgot to cc scott

On Wed, Jul 27, 2011 at 1:55 PM, Arek Kasprzyk <[hidden email]> wrote:

> Junjun:
> chado schema is publically available and i have done quite a bit of
> work with it in the past.
> The end result was that MBuilder could support 3NF transformation
> quite well but this was not sufficient for chado.
> Chado is a schema with a lot of recursive self-referencing based
> around 'feature' table. This, of course, can still be transformed
> using 3NF algorithm but the end result will not be as exiciting as one
> would like to. I experimented with it a bit a few years ago and came
> up with an alternative to 3NF algorihm which would work much better
> with chado. However given that current MConfigurator has not even
> acquired all the MBuilder features this seems to be a long way ahead.
> It will be better if you concentrate on implementing basic features
> for MConfigurator to get 3NF going properly first. This will give you
> the basics for chado. Once this is sorted out I"ll be glad to help
> with a proper algorithm for chado transformation
>
>
> a
>
>
>
> On Tue, Jul 26, 2011 at 12:01 PM, Junjun Zhang <[hidden email]> wrote:
>> Hi Aminah,
>>
>> Is that chado schema publicly available? It would be very helpful if we can test it out here.
>>
>> Also, I am just curious how your current mart is built. If you'd like to try 0.8 with the existing mart db, you can directly import it using martconfigurator.
>>
>> Best regards,
>>
>> Junjun
>> Sent from my BBerry
>>
>> ----- Original Message -----
>> From: Aminah Keliet [mailto:[hidden email]]
>> Sent: Tuesday, July 26, 2011 10:34 AM
>> To: [hidden email] <[hidden email]>
>> Subject: [BioMart Users] biomart v0.8 : error creating mart from Chado schema
>>
>> Hi
>>
>> We are testing the new version of Biomart (0.8 rc 6) to replace our
>> current install (v 0.7). We build mart on the GMOD-Chado schema using
>> the feature table as main table for our marts. With the new version we
>> get an error when we try to do the same thing. In the Add data source
>> panel, we choose the feature table from the public schema, then we click
>> add and we get :
>>
>> [AWT-EventQueue-1] INFO martconfigurator - Done saving settings
>> [Thread-104] INFO martconfigurator - Initialize source schema
>> [Thread-104] INFO martconfigurator - Done synchronising
>> [Thread-104] ERROR martconfigurator - duplicated relation
>> feature.[feature_id_1057] -> feature__feature_genotype.[feature_id_1057]
>> [AWT-EventQueue-1] ERROR martconfigurator - Exception occurred in
>> MartBuilder
>> org.biomart.common.exceptions.BioMartError:
>> org.biomart.common.exceptions.AssociationException: A relation between
>> these two keys already exists.
>>    at
>> org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:231)
>>    at
>> org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:369)
>>    at
>> org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:484)
>>    at
>> org.biomart.configurator.controller.MartController.synchronise(MartController.java:900)
>>    at
>> org.biomart.configurator.controller.MartController.suggestMarts(MartController.java:1375)
>>    at
>> org.biomart.configurator.controller.MartController.requestCreateMartsFromSource(MartController.java:1599)
>>    at
>> org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:98)
>>    at
>> org.biomart.configurator.view.component.container.SourceGroupPanel$1.construct(SourceGroupPanel.java:85)
>>    at org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128)
>>    at java.lang.Thread.run(Thread.java:619)
>> Caused by: org.biomart.common.exceptions.AssociationException: A
>> relation between these two keys already exists.
>>    at org.biomart.objects.objects.Relation.<init>(Relation.java:141)
>>    at
>> org.biomart.objects.objects.RelationTarget.<init>(RelationTarget.java:17)
>>    at
>> org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:225)
>>    ... 9 more
>>
>> Do you have any idea ?
>> Thanks
>>
>> --
>> Aminah Olivia KELIET
>> Ingenieur d'études en Bio-informatique
>>
>> Unité de recherche en Génomique-Info
>> INRA Centre de Versailles
>> Route de Saint Cyr
>> 78026 Versailles Cedex
>>
>> email: [hidden email]
>> url:http://urgi.versailles.inra.fr
>> tel: 01.30.83.37.74
>>
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
>>
>
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Re: [BioMart Users] biomart v0.8 : error creating mart from Chado schema

Junjun Zhang
In reply to this post by Arek Kasprzyk
Hi Arek,


Thanks for sharing your insightful information. Yes, we will concentrate
on implementing transforming 3NF schema first.

Cheers,
Junjun



On 11-07-27 1:55 PM, "Arek Kasprzyk" <[hidden email]> wrote:

>Junjun:
>chado schema is publically available and i have done quite a bit of
>work with it in the past.
>The end result was that MBuilder could support 3NF transformation
>quite well but this was not sufficient for chado.
>Chado is a schema with a lot of recursive self-referencing based
>around 'feature' table. This, of course, can still be transformed
>using 3NF algorithm but the end result will not be as exiciting as one
>would like to. I experimented with it a bit a few years ago and came
>up with an alternative to 3NF algorihm which would work much better
>with chado. However given that current MConfigurator has not even
>acquired all the MBuilder features this seems to be a long way ahead.
>It will be better if you concentrate on implementing basic features
>for MConfigurator to get 3NF going properly first. This will give you
>the basics for chado. Once this is sorted out I"ll be glad to help
>with a proper algorithm for chado transformation
>
>
>a
>
>
>
>On Tue, Jul 26, 2011 at 12:01 PM, Junjun Zhang <[hidden email]>
>wrote:
>> Hi Aminah,
>>
>> Is that chado schema publicly available? It would be very helpful if we
>>can test it out here.
>>
>> Also, I am just curious how your current mart is built. If you'd like
>>to try 0.8 with the existing mart db, you can directly import it using
>>martconfigurator.
>>
>> Best regards,
>>
>> Junjun
>> Sent from my BBerry
>>
>> ----- Original Message -----
>> From: Aminah Keliet [mailto:[hidden email]]
>> Sent: Tuesday, July 26, 2011 10:34 AM
>> To: [hidden email] <[hidden email]>
>> Subject: [BioMart Users] biomart v0.8 : error creating mart from Chado
>>schema
>>
>> Hi
>>
>> We are testing the new version of Biomart (0.8 rc 6) to replace our
>> current install (v 0.7). We build mart on the GMOD-Chado schema using
>> the feature table as main table for our marts. With the new version we
>> get an error when we try to do the same thing. In the Add data source
>> panel, we choose the feature table from the public schema, then we click
>> add and we get :
>>
>> [AWT-EventQueue-1] INFO martconfigurator - Done saving settings
>> [Thread-104] INFO martconfigurator - Initialize source schema
>> [Thread-104] INFO martconfigurator - Done synchronising
>> [Thread-104] ERROR martconfigurator - duplicated relation
>> feature.[feature_id_1057] -> feature__feature_genotype.[feature_id_1057]
>> [AWT-EventQueue-1] ERROR martconfigurator - Exception occurred in
>> MartBuilder
>> org.biomart.common.exceptions.BioMartError:
>> org.biomart.common.exceptions.AssociationException: A relation between
>> these two keys already exists.
>>    at
>>
>>org.biomart.configurator.controller.MartController.processParentDatasetTa
>>ble(MartController.java:231)
>>    at
>>
>>org.biomart.configurator.controller.MartController.generateDatasetTable(M
>>artController.java:369)
>>    at
>>
>>org.biomart.configurator.controller.MartController.generateDatasetTable(M
>>artController.java:484)
>>    at
>>
>>org.biomart.configurator.controller.MartController.synchronise(MartContro
>>ller.java:900)
>>    at
>>
>>org.biomart.configurator.controller.MartController.suggestMarts(MartContr
>>oller.java:1375)
>>    at
>>
>>org.biomart.configurator.controller.MartController.requestCreateMartsFrom
>>Source(MartController.java:1599)
>>    at
>>
>>org.biomart.configurator.controller.ObjectController.initMarts(ObjectCont
>>roller.java:98)
>>    at
>>
>>org.biomart.configurator.view.component.container.SourceGroupPanel$1.cons
>>truct(SourceGroupPanel.java:85)
>>    at
>>org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128)
>>    at java.lang.Thread.run(Thread.java:619)
>> Caused by: org.biomart.common.exceptions.AssociationException: A
>> relation between these two keys already exists.
>>    at org.biomart.objects.objects.Relation.<init>(Relation.java:141)
>>    at
>>
>>org.biomart.objects.objects.RelationTarget.<init>(RelationTarget.java:17)
>>    at
>>
>>org.biomart.configurator.controller.MartController.processParentDatasetTa
>>ble(MartController.java:225)
>>    ... 9 more
>>
>> Do you have any idea ?
>> Thanks
>>
>> --
>> Aminah Olivia KELIET
>> Ingenieur d'études en Bio-informatique
>>
>> Unité de recherche en Génomique-Info
>> INRA Centre de Versailles
>> Route de Saint Cyr
>> 78026 Versailles Cedex
>>
>> email: [hidden email]
>> url:http://urgi.versailles.inra.fr
>> tel: 01.30.83.37.74
>>
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
>>

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Re: [BioMart Users] biomart v0.8 : error creating mart from Chado schema

Joachim Baran-2
Hi!

  Aminah, do you use a very simple Chado set-up where you do not populate
the feature (or other) tables with recursively linked data?

  From your email it sounded like you had already build an BioMart 0.7
mart from your Chado database. If your feature table contains only "flat"
data (features are not linked via the feature_relationship table), then
you should still be able to create a mart of your database.

  Can you please check whether this is the case? I somehow doubt it
though, because one of the main aspects of Chado are the graph structures
it entails.

Joachim

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Re: [BioMart Users] biomart v0.8 : error creating mart from Chado schema

Arek Kasprzyk
Joachim:
Yes, you can certainly transform any chado to mart using a standard
3NF transformation algorithm as currently implemented in 0.7 MBuilder.
It will work 'mechanically'. You will be able to configure it and
query the data. However, it will look 'weird' to a biologist because
as you say there is a lot recursive stuff going on and this will not
get flattened by 3NF transformation alone.
To 'really' transform chado you will need an extension to the current
3NF algorithm which first flattens all the recursive structures and
only then applies 3NF transform. I implemented it once in the MBuilder
prototype and it worked oK but it never made it the final MBuilder
implementation.


a






On Wed, Jul 27, 2011 at 3:11 PM, Joachim Baran <[hidden email]> wrote:

> Hi!
>
>  Aminah, do you use a very simple Chado set-up where you do not populate
> the feature (or other) tables with recursively linked data?
>
>  From your email it sounded like you had already build an BioMart 0.7
> mart from your Chado database. If your feature table contains only "flat"
> data (features are not linked via the feature_relationship table), then
> you should still be able to create a mart of your database.
>
>  Can you please check whether this is the case? I somehow doubt it
> though, because one of the main aspects of Chado are the graph structures
> it entails.
>
> Joachim
>
>
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