[biomart-users] Load a Chado database into BioMart 0.9

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[biomart-users] Load a Chado database into BioMart 0.9

Justine Dardaillon
Hello,

We are actually working on BioMart server 0.9 and we want to integrate our Chado database ANISEED (http://www.aniseed.cnrs.fr/) in order to deploy the BioMart server on our website. But we encountered an issue when we want to Add Source with the "Add Source Wizard", after clicking on "Finish", an error occured. Even if we try to load the classic Chado database empty, we receive the same error message :


"""
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:219)
    at org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:343)
    at org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:442)
    at org.biomart.configurator.controller.MartController.synchronise(MartController.java:818)
    at org.biomart.configurator.controller.MartController.suggestMarts(MartController.java:1504)
    at org.biomart.configurator.controller.MartController.requestCreateMartsFromSource(MartController.java:1710)
    at org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:98)
    at org.biomart.configurator.view.component.container.SourceGroupPanel$1.doInBackground(SourceGroupPanel.java:117)
    at org.biomart.configurator.view.component.container.SourceGroupPanel$1.doInBackground(SourceGroupPanel.java:112)
    at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at javax.swing.SwingWorker.run(SwingWorker.java:334)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.biomart.common.exceptions.AssociationException: A relation between these two keys already exists.
    at org.biomart.objects.objects.Relation.<init>(Relation.java:166)
    at org.biomart.objects.objects.RelationTarget.<init>(RelationTarget.java:17)
    at org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:213)
    ... 14 more

"""

Is there any solutions for this problem on BioMart 0.9 ? Or should we use BioMart 0.7 and try to follow the tutorial made by INRA URGI's team a few years ago ?

Thank you for your help,

Best Regards,


-- Justine Dardaillon ANISEED TEAM Centre de Recherche de Biologie cellulaire de Montpellier CRBM -- CNRS UMR 5237 1919 Route de Mende 34293 Montpellier Cedex 5 FRANCE http://www.crbm.cnrs.fr/ http://www.aniseed.cnrs.fr/

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Re: [biomart-users] Load a Chado database into BioMart 0.9

Arek Kasprzyk
Hi Justine,

I vaguely remember that chado schema does not strictly adhere to the 3NF and there is a bit self referencing with the keys going on there? I guess this might cause some issues. I would be quite interested to see how the INRA URGI's team bypassed this problem. Would you be able to point me to this tutorial so i can check how this relates to 0.7 vs 0.9 implementation?

Arek

On 10 June 2016 at 08:26, Justine Dardaillon <[hidden email]> wrote:
Hello,

We are actually working on BioMart server 0.9 and we want to integrate our Chado database ANISEED (http://www.aniseed.cnrs.fr/) in order to deploy the BioMart server on our website. But we encountered an issue when we want to Add Source with the "Add Source Wizard", after clicking on "Finish", an error occured. Even if we try to load the classic Chado database empty, we receive the same error message :


"""
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:219)
    at org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:343)
    at org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:442)
    at org.biomart.configurator.controller.MartController.synchronise(MartController.java:818)
    at org.biomart.configurator.controller.MartController.suggestMarts(MartController.java:1504)
    at org.biomart.configurator.controller.MartController.requestCreateMartsFromSource(MartController.java:1710)
    at org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:98)
    at org.biomart.configurator.view.component.container.SourceGroupPanel$1.doInBackground(SourceGroupPanel.java:117)
    at org.biomart.configurator.view.component.container.SourceGroupPanel$1.doInBackground(SourceGroupPanel.java:112)
    at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at javax.swing.SwingWorker.run(SwingWorker.java:334)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.biomart.common.exceptions.AssociationException: A relation between these two keys already exists.
    at org.biomart.objects.objects.Relation.<init>(Relation.java:166)
    at org.biomart.objects.objects.RelationTarget.<init>(RelationTarget.java:17)
    at org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:213)
    ... 14 more

"""

Is there any solutions for this problem on BioMart 0.9 ? Or should we use BioMart 0.7 and try to follow the tutorial made by INRA URGI's team a few years ago ?

Thank you for your help,

Best Regards,


-- Justine Dardaillon ANISEED TEAM Centre de Recherche de Biologie cellulaire de Montpellier CRBM -- CNRS UMR 5237 1919 Route de Mende 34293 Montpellier Cedex 5 FRANCE http://www.crbm.cnrs.fr/ http://www.aniseed.cnrs.fr/

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Re: [biomart-users] Load a Chado database into BioMart 0.9

Justine Dardaillon
Hi Arek,

Yes, Chado schema does contain some recursive links, for example a feature could be a part of a feature, but even when the feature and feature-relationship tables are empty (and even if we take the Chado database without put any data in it and without modify something) it doesn't work and we obtain the same error mentionned before. I send you the link of the tutorial below :

http://gmod.org/mediawiki/images/8/8d/How_to_load_chado_to_biomart.pdf

I hope it will help,

Justine.



Le vendredi 10 juin 2016 11:04:41 UTC+2, Arek Kasprzyk a écrit :
Hi Justine,

I vaguely remember that chado schema does not strictly adhere to the 3NF and there is a bit self referencing with the keys going on there? I guess this might cause some issues. I would be quite interested to see how the INRA URGI's team bypassed this problem. Would you be able to point me to this tutorial so i can check how this relates to 0.7 vs 0.9 implementation?

Arek

On 10 June 2016 at 08:26, Justine Dardaillon <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="FD6VnX6RAwAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">justine7....@...> wrote:
Hello,

We are actually working on BioMart server 0.9 and we want to integrate our Chado database ANISEED (<a href="http://www.aniseed.cnrs.fr/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.aniseed.cnrs.fr%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGWHW9woiTg9jS8e-4N41hZKEa48Q&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.aniseed.cnrs.fr%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGWHW9woiTg9jS8e-4N41hZKEa48Q&#39;;return true;">http://www.aniseed.cnrs.fr/) in order to deploy the BioMart server on our website. But we encountered an issue when we want to Add Source with the "Add Source Wizard", after clicking on "Finish", an error occured. Even if we try to load the classic Chado database empty, we receive the same error message :


"""
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:219)
    at org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:343)
    at org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:442)
    at org.biomart.configurator.controller.MartController.synchronise(MartController.java:818)
    at org.biomart.configurator.controller.MartController.suggestMarts(MartController.java:1504)
    at org.biomart.configurator.controller.MartController.requestCreateMartsFromSource(MartController.java:1710)
    at org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:98)
    at org.biomart.configurator.view.component.container.SourceGroupPanel$1.doInBackground(SourceGroupPanel.java:117)
    at org.biomart.configurator.view.component.container.SourceGroupPanel$1.doInBackground(SourceGroupPanel.java:112)
    at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at javax.swing.SwingWorker.run(SwingWorker.java:334)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.biomart.common.exceptions.AssociationException: A relation between these two keys already exists.
    at org.biomart.objects.objects.Relation.<init>(Relation.java:166)
    at org.biomart.objects.objects.RelationTarget.<init>(RelationTarget.java:17)
    at org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:213)
    ... 14 more

"""

Is there any solutions for this problem on BioMart 0.9 ? Or should we use BioMart 0.7 and try to follow the tutorial made by INRA URGI's team a few years ago ?

Thank you for your help,

Best Regards,


-- Justine Dardaillon ANISEED TEAM Centre de Recherche de Biologie cellulaire de Montpellier CRBM -- CNRS UMR 5237 1919 Route de Mende 34293 Montpellier Cedex 5 FRANCE <a href="http://www.crbm.cnrs.fr/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.crbm.cnrs.fr%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGWCMXMrCcsQtFvzWM_Pm64CoD0Cg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.crbm.cnrs.fr%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGWCMXMrCcsQtFvzWM_Pm64CoD0Cg&#39;;return true;">http://www.crbm.cnrs.fr/ <a href="http://www.aniseed.cnrs.fr/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.aniseed.cnrs.fr%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGWHW9woiTg9jS8e-4N41hZKEa48Q&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.aniseed.cnrs.fr%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGWHW9woiTg9jS8e-4N41hZKEa48Q&#39;;return true;">http://www.aniseed.cnrs.fr/

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Re: [biomart-users] Load a Chado database into BioMart 0.9

Arek Kasprzyk
Hi Justine,

Thanks for the pointer to this useful tutorial. I had a quick look and don't see anything there that would be chado specific so in theory this should be working with 0.9 just the same (However, as you said you ran into some problems).

If you still prefer to use 0.9 than i would suggest that we can bypass this problem as follows:

1. Download 0.7 martj only (please note that the location of the repo has now changed to https://github.com/biomart/martj).
2. Follow the section 'Dataset creation' (pages 6-8) only until your new database is created, then:

3. Download 0.9 and configure your new mart using MartConfigurator (choosing the source option: "RDBMS", "relational mart")

Hopefully, this should fix the problem

a.













On 10 June 2016 at 10:49, Justine Dardaillon <[hidden email]> wrote:
Hi Arek,

Yes, Chado schema does contain some recursive links, for example a feature could be a part of a feature, but even when the feature and feature-relationship tables are empty (and even if we take the Chado database without put any data in it and without modify something) it doesn't work and we obtain the same error mentionned before. I send you the link of the tutorial below :

http://gmod.org/mediawiki/images/8/8d/How_to_load_chado_to_biomart.pdf

I hope it will help,

Justine.



Le vendredi 10 juin 2016 11:04:41 UTC+2, Arek Kasprzyk a écrit :
Hi Justine,

I vaguely remember that chado schema does not strictly adhere to the 3NF and there is a bit self referencing with the keys going on there? I guess this might cause some issues. I would be quite interested to see how the INRA URGI's team bypassed this problem. Would you be able to point me to this tutorial so i can check how this relates to 0.7 vs 0.9 implementation?

Arek

On 10 June 2016 at 08:26, Justine Dardaillon <[hidden email]> wrote:
Hello,

We are actually working on BioMart server 0.9 and we want to integrate our Chado database ANISEED (http://www.aniseed.cnrs.fr/) in order to deploy the BioMart server on our website. But we encountered an issue when we want to Add Source with the "Add Source Wizard", after clicking on "Finish", an error occured. Even if we try to load the classic Chado database empty, we receive the same error message :


"""
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:219)
    at org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:343)
    at org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:442)
    at org.biomart.configurator.controller.MartController.synchronise(MartController.java:818)
    at org.biomart.configurator.controller.MartController.suggestMarts(MartController.java:1504)
    at org.biomart.configurator.controller.MartController.requestCreateMartsFromSource(MartController.java:1710)
    at org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:98)
    at org.biomart.configurator.view.component.container.SourceGroupPanel$1.doInBackground(SourceGroupPanel.java:117)
    at org.biomart.configurator.view.component.container.SourceGroupPanel$1.doInBackground(SourceGroupPanel.java:112)
    at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at javax.swing.SwingWorker.run(SwingWorker.java:334)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.biomart.common.exceptions.AssociationException: A relation between these two keys already exists.
    at org.biomart.objects.objects.Relation.<init>(Relation.java:166)
    at org.biomart.objects.objects.RelationTarget.<init>(RelationTarget.java:17)
    at org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:213)
    ... 14 more

"""

Is there any solutions for this problem on BioMart 0.9 ? Or should we use BioMart 0.7 and try to follow the tutorial made by INRA URGI's team a few years ago ?

Thank you for your help,

Best Regards,


-- Justine Dardaillon ANISEED TEAM Centre de Recherche de Biologie cellulaire de Montpellier CRBM -- CNRS UMR 5237 1919 Route de Mende 34293 Montpellier Cedex 5 FRANCE http://www.crbm.cnrs.fr/ http://www.aniseed.cnrs.fr/

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Re: [biomart-users] Load a Chado database into BioMart 0.9

Justine Dardaillon

Hi, Arek,

Thank you for your help, we will try to do this. My team and I have some questions about Biomart and its future.
First do you plan to update Biomart 0.7 or 0.9  to be used with the more recent versions of Java as we already had problems and, for Biomart 0.7, had to downgrade Postgres 9.5 to 9.1 due to the problem with the Java and database driver, and also Java to version 6 to be able to install Biomart 0.7, also do you plan to update the version 0.9 to be able to import  Chado tables more easily as the version 0.7 can do (hopefully). In general do you plan on other future development, it would be nice to keep these things alive both for us, and the future development and compatibility of Biomart with progressing platforms it works with.

with best wishes,
Justine

Le mercredi 15 juin 2016 16:54:57 UTC+2, Arek Kasprzyk a écrit :
Hi Justine,

Thanks for the pointer to this useful tutorial. I had a quick look and don't see anything there that would be chado specific so in theory this should be working with 0.9 just the same (However, as you said you ran into some problems).

If you still prefer to use 0.9 than i would suggest that we can bypass this problem as follows:

1. Download 0.7 martj only (please note that the location of the repo has now changed to <a href="https://github.com/biomart/martj" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Fbiomart%2Fmartj\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFfRfpeZ1oPUNydLb--_Pm9GIlU6A&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Fbiomart%2Fmartj\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFfRfpeZ1oPUNydLb--_Pm9GIlU6A&#39;;return true;">https://github.com/biomart/martj).
2. Follow the section 'Dataset creation' (pages 6-8) only until your new database is created, then:

3. Download 0.9 and configure your new mart using MartConfigurator (choosing the source option: "RDBMS", "relational mart")

Hopefully, this should fix the problem

a.













On 10 June 2016 at 10:49, Justine Dardaillon <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="qJtqblpeAQAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">justine7....@...> wrote:
Hi Arek,

Yes, Chado schema does contain some recursive links, for example a feature could be a part of a feature, but even when the feature and feature-relationship tables are empty (and even if we take the Chado database without put any data in it and without modify something) it doesn't work and we obtain the same error mentionned before. I send you the link of the tutorial below :

<a href="http://gmod.org/mediawiki/images/8/8d/How_to_load_chado_to_biomart.pdf" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fgmod.org%2Fmediawiki%2Fimages%2F8%2F8d%2FHow_to_load_chado_to_biomart.pdf\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGdI_CkyLINxEv6O4FE10ijcCYYgw&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fgmod.org%2Fmediawiki%2Fimages%2F8%2F8d%2FHow_to_load_chado_to_biomart.pdf\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGdI_CkyLINxEv6O4FE10ijcCYYgw&#39;;return true;">http://gmod.org/mediawiki/images/8/8d/How_to_load_chado_to_biomart.pdf

I hope it will help,

Justine.



Le vendredi 10 juin 2016 11:04:41 UTC+2, Arek Kasprzyk a écrit :
Hi Justine,

I vaguely remember that chado schema does not strictly adhere to the 3NF and there is a bit self referencing with the keys going on there? I guess this might cause some issues. I would be quite interested to see how the INRA URGI's team bypassed this problem. Would you be able to point me to this tutorial so i can check how this relates to 0.7 vs 0.9 implementation?

Arek

On 10 June 2016 at 08:26, Justine Dardaillon <[hidden email]> wrote:
Hello,

We are actually working on BioMart server 0.9 and we want to integrate our Chado database ANISEED (<a href="http://www.aniseed.cnrs.fr/" rel="nofollow" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.aniseed.cnrs.fr%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGWHW9woiTg9jS8e-4N41hZKEa48Q&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.aniseed.cnrs.fr%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGWHW9woiTg9jS8e-4N41hZKEa48Q&#39;;return true;">http://www.aniseed.cnrs.fr/) in order to deploy the BioMart server on our website. But we encountered an issue when we want to Add Source with the "Add Source Wizard", after clicking on "Finish", an error occured. Even if we try to load the classic Chado database empty, we receive the same error message :


"""
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:219)
    at org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:343)
    at org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:442)
    at org.biomart.configurator.controller.MartController.synchronise(MartController.java:818)
    at org.biomart.configurator.controller.MartController.suggestMarts(MartController.java:1504)
    at org.biomart.configurator.controller.MartController.requestCreateMartsFromSource(MartController.java:1710)
    at org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:98)
    at org.biomart.configurator.view.component.container.SourceGroupPanel$1.doInBackground(SourceGroupPanel.java:117)
    at org.biomart.configurator.view.component.container.SourceGroupPanel$1.doInBackground(SourceGroupPanel.java:112)
    at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at javax.swing.SwingWorker.run(SwingWorker.java:334)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.biomart.common.exceptions.AssociationException: A relation between these two keys already exists.
    at org.biomart.objects.objects.Relation.<init>(Relation.java:166)
    at org.biomart.objects.objects.RelationTarget.<init>(RelationTarget.java:17)
    at org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:213)
    ... 14 more

"""

Is there any solutions for this problem on BioMart 0.9 ? Or should we use BioMart 0.7 and try to follow the tutorial made by INRA URGI's team a few years ago ?

Thank you for your help,

Best Regards,


-- Justine Dardaillon ANISEED TEAM Centre de Recherche de Biologie cellulaire de Montpellier CRBM -- CNRS UMR 5237 1919 Route de Mende 34293 Montpellier Cedex 5 FRANCE <a href="http://www.crbm.cnrs.fr/" rel="nofollow" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.crbm.cnrs.fr%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGWCMXMrCcsQtFvzWM_Pm64CoD0Cg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.crbm.cnrs.fr%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGWCMXMrCcsQtFvzWM_Pm64CoD0Cg&#39;;return true;">http://www.crbm.cnrs.fr/ <a href="http://www.aniseed.cnrs.fr/" rel="nofollow" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.aniseed.cnrs.fr%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGWHW9woiTg9jS8e-4N41hZKEa48Q&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.aniseed.cnrs.fr%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGWHW9woiTg9jS8e-4N41hZKEa48Q&#39;;return true;">http://www.aniseed.cnrs.fr/

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Re: [biomart-users] Load a Chado database into BioMart 0.9

Arek Kasprzyk
Hi Justine,

We have made a one luke warm attempt to upgrade it to the more recent version of Java in the recent past but ran into some annoying 'non-response' problem with one of the MConfigurator panels. However, this is something that we are definitely planning to do. We just need to put more effort into it but unfortunately being rather short-staffed ATM.

a.


On 17 June 2016 at 08:52, Justine Dardaillon <[hidden email]> wrote:

Hi, Arek,

Thank you for your help, we will try to do this. My team and I have some questions about Biomart and its future.
First do you plan to update Biomart 0.7 or 0.9  to be used with the more recent versions of Java as we already had problems and, for Biomart 0.7, had to downgrade Postgres 9.5 to 9.1 due to the problem with the Java and database driver, and also Java to version 6 to be able to install Biomart 0.7, also do you plan to update the version 0.9 to be able to import  Chado tables more easily as the version 0.7 can do (hopefully). In general do you plan on other future development, it would be nice to keep these things alive both for us, and the future development and compatibility of Biomart with progressing platforms it works with.

with best wishes,
Justine

Le mercredi 15 juin 2016 16:54:57 UTC+2, Arek Kasprzyk a écrit :
Hi Justine,

Thanks for the pointer to this useful tutorial. I had a quick look and don't see anything there that would be chado specific so in theory this should be working with 0.9 just the same (However, as you said you ran into some problems).

If you still prefer to use 0.9 than i would suggest that we can bypass this problem as follows:

1. Download 0.7 martj only (please note that the location of the repo has now changed to https://github.com/biomart/martj).
2. Follow the section 'Dataset creation' (pages 6-8) only until your new database is created, then:

3. Download 0.9 and configure your new mart using MartConfigurator (choosing the source option: "RDBMS", "relational mart")

Hopefully, this should fix the problem

a.













On 10 June 2016 at 10:49, Justine Dardaillon <[hidden email]> wrote:
Hi Arek,

Yes, Chado schema does contain some recursive links, for example a feature could be a part of a feature, but even when the feature and feature-relationship tables are empty (and even if we take the Chado database without put any data in it and without modify something) it doesn't work and we obtain the same error mentionned before. I send you the link of the tutorial below :

http://gmod.org/mediawiki/images/8/8d/How_to_load_chado_to_biomart.pdf

I hope it will help,

Justine.



Le vendredi 10 juin 2016 11:04:41 UTC+2, Arek Kasprzyk a écrit :
Hi Justine,

I vaguely remember that chado schema does not strictly adhere to the 3NF and there is a bit self referencing with the keys going on there? I guess this might cause some issues. I would be quite interested to see how the INRA URGI's team bypassed this problem. Would you be able to point me to this tutorial so i can check how this relates to 0.7 vs 0.9 implementation?

Arek

On 10 June 2016 at 08:26, Justine Dardaillon <[hidden email]> wrote:
Hello,

We are actually working on BioMart server 0.9 and we want to integrate our Chado database ANISEED (http://www.aniseed.cnrs.fr/) in order to deploy the BioMart server on our website. But we encountered an issue when we want to Add Source with the "Add Source Wizard", after clicking on "Finish", an error occured. Even if we try to load the classic Chado database empty, we receive the same error message :


"""
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:219)
    at org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:343)
    at org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:442)
    at org.biomart.configurator.controller.MartController.synchronise(MartController.java:818)
    at org.biomart.configurator.controller.MartController.suggestMarts(MartController.java:1504)
    at org.biomart.configurator.controller.MartController.requestCreateMartsFromSource(MartController.java:1710)
    at org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:98)
    at org.biomart.configurator.view.component.container.SourceGroupPanel$1.doInBackground(SourceGroupPanel.java:117)
    at org.biomart.configurator.view.component.container.SourceGroupPanel$1.doInBackground(SourceGroupPanel.java:112)
    at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at javax.swing.SwingWorker.run(SwingWorker.java:334)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.biomart.common.exceptions.AssociationException: A relation between these two keys already exists.
    at org.biomart.objects.objects.Relation.<init>(Relation.java:166)
    at org.biomart.objects.objects.RelationTarget.<init>(RelationTarget.java:17)
    at org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:213)
    ... 14 more

"""

Is there any solutions for this problem on BioMart 0.9 ? Or should we use BioMart 0.7 and try to follow the tutorial made by INRA URGI's team a few years ago ?

Thank you for your help,

Best Regards,


-- Justine Dardaillon ANISEED TEAM Centre de Recherche de Biologie cellulaire de Montpellier CRBM -- CNRS UMR 5237 1919 Route de Mende 34293 Montpellier Cedex 5 FRANCE http://www.crbm.cnrs.fr/ http://www.aniseed.cnrs.fr/

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