Upgrade from Tripal v2.x to v3.x

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Upgrade from Tripal v2.x to v3.x

vijaya tsavatapalli
Hi Stephen,

I am using Tripal 7.x-3.0-alpha1+198-dev version, all the modules were upgraded to V3.0 successfully but when i am trying to prepare chado and upgrade existing Chado v1.2 to v1.3(no data is lost) I was ran into an error.

 Please see the attachment, i am using postgres 9.4.4.

Thanks,
Vijaya



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Re: Upgrade from Tripal v2.x to v3.x

Stephen Ficklin-2
Hi Vijaya,

I think I see what's going on.  There is a view in your PostgreSQL
implementation that is using the feature table.   In the Chado v1.3
upgrade, many of the Integer fields (primary keys and foreign keys) were
changed to "bigints" to accommodate larger number of records.  
Unfortunately, altering a table to change a column from int to bigint
hits this problem when there is a PostgreSQL View that uses the table.  
Chado itself comes with a lot of views.  So, in the upgrade script we
actually remove the views, adjust the tables and then recreate the views
to get around this problem.   So, the problem here is one of two cases:
1)  we have missed a view in our upgrade script or 2) you have a custom
view that is not part of Chado but that uses the feature table.

Can you verify which of this might be causing the problem for you?

Stephen


On 6/23/2016 6:48 AM, vijaya tsavatapalli wrote:

> Hi Stephen,
>
> I am using Tripal 7.x-3.0-alpha1+198-dev version, all the modules were
> upgraded to V3.0 successfully but when i am trying to prepare chado
> and upgrade existing Chado v1.2 to v1.3(no data is lost) I was ran
> into an error.
>
>  Please see the attachment, i am using postgres 9.4.4.
>
> Thanks,
> Vijaya
>
>


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Re: Upgrade from Tripal v2.x to v3.x

vijaya tsavatapalli
Hi Stephen,

I don't have a custom view that uses feature table.  On the install chado page i see a statement "Please note: the upgrade of Chado from v1.2 to v1.3 may require a fix to your materialized views." .  Please find the complete error in the  attachment and also attachment for materialized views i had for my site.

Thanks,
Vijaya

On Thu, Jun 23, 2016 at 1:03 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Vijaya,

I think I see what's going on.  There is a view in your PostgreSQL implementation that is using the feature table.   In the Chado v1.3 upgrade, many of the Integer fields (primary keys and foreign keys) were changed to "bigints" to accommodate larger number of records.   Unfortunately, altering a table to change a column from int to bigint hits this problem when there is a PostgreSQL View that uses the table.   Chado itself comes with a lot of views.  So, in the upgrade script we actually remove the views, adjust the tables and then recreate the views to get around this problem.   So, the problem here is one of two cases: 1)  we have missed a view in our upgrade script or 2) you have a custom view that is not part of Chado but that uses the feature table.

Can you verify which of this might be causing the problem for you?

Stephen



On 6/23/2016 6:48 AM, vijaya tsavatapalli wrote:
Hi Stephen,

I am using Tripal 7.x-3.0-alpha1+198-dev version, all the modules were upgraded to V3.0 successfully but when i am trying to prepare chado and upgrade existing Chado v1.2 to v1.3(no data is lost) I was ran into an error.

 Please see the attachment, i am using postgres 9.4.4.

Thanks,
Vijaya





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Re: Upgrade from Tripal v2.x to v3.x

Stephen Ficklin-2

Hi Vijaya (and Scott see further down),

I think I've figured out the problem.... Looking more closely at your original email I see that the view so.unorient_intra_transposition is what is causing the problem for you.  It is present in the Chado v1.11 schema, but not in the Chado v1.2 schema.  Therefore the upgrade script that moves Chado from v1.2 to v1.3 does not account for that view and the upgrade crashes. 

I'm CC'ing Scott to see if he knows if that view was purposely removed from Chado v1.2 or if it should be present or if the upgrade script should remove it.  I'm not sure what it's for.   In any event, if you delete that view, and as long as there are no others like this one then the upgrade will move past this. 

I've added an issue to our Tripal Issue queue to deal with it:

https://www.drupal.org/node/2754831

If in your testing, you come across any more of these views would you mind commenting on the Issue linked to above to let us know?

Just a clarification... the materialized views are different from PostgreSQL views and they don't have the same problem when upgrading Chado.  Although, as the message indicates they may still need fixing.  But that fix can be applied after the upgrade and shouldn't cause errors.  The problem is with PostgreSQL Views.  I've adjusted the warning message in Tripal to make this distinction. 

Stephen


On 6/23/2016 11:17 AM, vijaya tsavatapalli wrote:
Hi Stephen,

I don't have a custom view that uses feature table.  On the install chado page i see a statement "Please note: the upgrade of Chado from v1.2 to v1.3 may require a fix to your materialized views." .  Please find the complete error in the  attachment and also attachment for materialized views i had for my site.

Thanks,
Vijaya

On Thu, Jun 23, 2016 at 1:03 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Vijaya,

I think I see what's going on.  There is a view in your PostgreSQL implementation that is using the feature table.   In the Chado v1.3 upgrade, many of the Integer fields (primary keys and foreign keys) were changed to "bigints" to accommodate larger number of records.   Unfortunately, altering a table to change a column from int to bigint hits this problem when there is a PostgreSQL View that uses the table.   Chado itself comes with a lot of views.  So, in the upgrade script we actually remove the views, adjust the tables and then recreate the views to get around this problem.   So, the problem here is one of two cases: 1)  we have missed a view in our upgrade script or 2) you have a custom view that is not part of Chado but that uses the feature table.

Can you verify which of this might be causing the problem for you?

Stephen



On 6/23/2016 6:48 AM, vijaya tsavatapalli wrote:
Hi Stephen,

I am using Tripal 7.x-3.0-alpha1+198-dev version, all the modules were upgraded to V3.0 successfully but when i am trying to prepare chado and upgrade existing Chado v1.2 to v1.3(no data is lost) I was ran into an error.

 Please see the attachment, i am using postgres 9.4.4.

Thanks,
Vijaya






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