Tripal 2 update errors

classic Classic list List threaded Threaded
20 messages Options
Reply | Threaded
Open this post in threaded view
|

Tripal 2 update errors

Michael Dondrup-3
Hi,

we are doing a test-run of the D6->7 migration of our site including a Tripal update, following http://tripal.info/tutorials/v2.0/upgrade

We are currently at step 14. Next, apply the Tripal updates: drush updatedb

All core updates, views and ctools have been performed without error and no pending db updates were scheduled prior to this step.


Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
does not exist
LINE 3: tripal_mviews tm
        ^

[...]
Drush command terminated abnormally due to an unrecoverable error.                              [error]
Error: Call to undefined function tripal_set_default_cv() in
/home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
The external command could not be executed due to an application error.                         [error]

I guess we have a fix for the first one, however that yields different errors:

The table tripal_mviews exists but in the schema chado. I tried to set the search_path back:
ALTER USER user SET search_path TO public, chado;

However this yields other errors:

Cannot add field tripal_custom_tables.mview_id: table doesn't exist.                            [error]
[...]
Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install on line 449
Drush command terminated abnormally due to an unrecoverable error.                              [error]
Error: Call to undefined function tripal_insert_obo() in
/home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install, line 449
The external command could not be executed due to an application error.                         [error]


I searched and found http://sourceforge.net/p/gmod/mailman/message/32762105/ but that doesn't seem to fit.

Best



Michael Dondrup
Researcher
Sea Lice Research Centre
Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen,
Norway


Full output of drush updatedb first iteration:

$ drush updatedb
The following updates are pending:

tripal_core module :
  7200 -   Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table  
  7201 -   Fixes missing language for nodes and URL aliases. This may take awhile...  
  7202 -   Adds a tripal_token_formats table for custom page titles and URL paths
  7203 -   Adds a tripal_toc table for customizing the table of contents on each Tripal page.
  7204 -   Adds the tripal_variable_terms and a tripal_node_variables tables

tripal_organism module :
  7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.  

tripal_cv module :
  7201 -   Fixes an error with the materialized view installation  

tripal_contact module :
  7200 -   This is the required update for tripal_contact when upgrading from Drupal core API 6.x.  
  7201 -   Adds missing foreign key constraints  
  7202 -   Updates path of tripal_contact OBO to be relative.

tripal_bulk_loader module :
  7200 -   Implements hook_update_N().   Update to 7.x-2.0  -Cast tripal_bulk_loader.template_id to int field  

tripal_library module :
  7200 -   This is the required update for tripal_library when upgrading from Drupal core API 6.x.  
  7201 -   Fixes an error with the materialized view installation  

tripal_stock module :
  7200 -   This is the required update for tripal_stock when upgrading from Drupal core API 6.x.  
  7201 -   Add materialized views

tripal_project module :
  7200 -   This is the required update for tripal_project when upgrading from Drupal core API 6.x.  

tripal_analysis module :
  7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.  
  7201 -   Fixes an error with the materialized view installation  

tripal_featuremap module :
  7200 -   This is the required update for tripal_featuremap when upgrading from Drupal core API 6.x.  This update may take some time to complete.
  7201 -   Adds missing foreign key constraints  
  7202 -   Fixes a typo when setting the default CV for the unittype_id field of the featuremap table.

tripal_feature module :
  7200 -   This is the required update for tripal_feature when upgrading from Drupal core API 6.x.  This update may take some time to complete.
  7201 -   Fixes an error with the materialized view installation  
  7202 -   Adds the temporary tables used for loading GFF files.

tripal_views module :
  7200 -   Tripal Views Update for 7.x-2.0    - Add relationship_only field to tripal_views_join    - Add relationship_handler field to tripal_views_join  

tripal_pub module :
  7202 -   Updates path of tripal_pub OBO to be relative.

Performed update: tripal_feature_update_7200                                                    [ok]
Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
does not exist
LINE 3: tripal_mviews tm
        ^
Performed update: tripal_feature_update_7201                                                    [ok]
Performed update: tripal_featuremap_update_7200                                                 [ok]
Performed update: tripal_featuremap_update_7201                                                 [ok]
PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655

Fatal error: Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
Drush command terminated abnormally due to an unrecoverable error.                              [error]
Error: Call to undefined function tripal_set_default_cv() in
/home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
The external command could not be executed due to an application error.                         [error]
Finished performing updates.                                                                    [ok]


---------------------------------------------------------------------------------------------------------------------------------------------
Full output after setting search_path to public, chado









------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Michael Dondrup-3
Hi,
we fixed the first problem somehow the tripal_custom_tables table was created in chado schema. I moved it
ALTER TABLE tripal_custom_tables SET SCHEMA public;

Leaving me with this error:

PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655


This is weird because the function is certainly defined in tripal/tripal_cv/api/tripal_cv.api.inc:function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE)

I have tried to drush cc all and even rebuilt the registry as described here: https://www.drupal.org/project/registry_rebuild

But to no avail. Anybody else having this problem?

I really appreciate your help.

Michael




On Jan 20, 2016, at 2:17 PM, Michael Dondrup wrote:

> Hi,
>
> we are doing a test-run of the D6->7 migration of our site including a Tripal update, following http://tripal.info/tutorials/v2.0/upgrade
>
> We are currently at step 14. Next, apply the Tripal updates: drush updatedb
>
> All core updates, views and ctools have been performed without error and no pending db updates were scheduled prior to this step.
>
>
> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
> does not exist
> LINE 3: tripal_mviews tm
>        ^
>
> [...]
> Drush command terminated abnormally due to an unrecoverable error.                              [error]
> Error: Call to undefined function tripal_set_default_cv() in
> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
> The external command could not be executed due to an application error.                         [error]
>
> I guess we have a fix for the first one, however that yields different errors:
>
> The table tripal_mviews exists but in the schema chado. I tried to set the search_path back:
> ALTER USER user SET search_path TO public, chado;
>
> However this yields other errors:
>
> Cannot add field tripal_custom_tables.mview_id: table doesn't exist.                            [error]
> [...]
> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install on line 449
> Drush command terminated abnormally due to an unrecoverable error.                              [error]
> Error: Call to undefined function tripal_insert_obo() in
> /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install, line 449
> The external command could not be executed due to an application error.                         [error]
>
>
> I searched and found http://sourceforge.net/p/gmod/mailman/message/32762105/ but that doesn't seem to fit.
>
> Best
>
>
>
> Michael Dondrup
> Researcher
> Sea Lice Research Centre
> Department of Informatics
> University of Bergen
> Thormøhlensgate 55, N-5008 Bergen,
> Norway
>
>
> Full output of drush updatedb first iteration:
>
> $ drush updatedb
> The following updates are pending:
>
> tripal_core module :
>  7200 -   Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table  
>  7201 -   Fixes missing language for nodes and URL aliases. This may take awhile...  
>  7202 -   Adds a tripal_token_formats table for custom page titles and URL paths
>  7203 -   Adds a tripal_toc table for customizing the table of contents on each Tripal page.
>  7204 -   Adds the tripal_variable_terms and a tripal_node_variables tables
>
> tripal_organism module :
>  7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.  
>
> tripal_cv module :
>  7201 -   Fixes an error with the materialized view installation  
>
> tripal_contact module :
>  7200 -   This is the required update for tripal_contact when upgrading from Drupal core API 6.x.  
>  7201 -   Adds missing foreign key constraints  
>  7202 -   Updates path of tripal_contact OBO to be relative.
>
> tripal_bulk_loader module :
>  7200 -   Implements hook_update_N().   Update to 7.x-2.0  -Cast tripal_bulk_loader.template_id to int field  
>
> tripal_library module :
>  7200 -   This is the required update for tripal_library when upgrading from Drupal core API 6.x.  
>  7201 -   Fixes an error with the materialized view installation  
>
> tripal_stock module :
>  7200 -   This is the required update for tripal_stock when upgrading from Drupal core API 6.x.  
>  7201 -   Add materialized views
>
> tripal_project module :
>  7200 -   This is the required update for tripal_project when upgrading from Drupal core API 6.x.  
>
> tripal_analysis module :
>  7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.  
>  7201 -   Fixes an error with the materialized view installation  
>
> tripal_featuremap module :
>  7200 -   This is the required update for tripal_featuremap when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>  7201 -   Adds missing foreign key constraints  
>  7202 -   Fixes a typo when setting the default CV for the unittype_id field of the featuremap table.
>
> tripal_feature module :
>  7200 -   This is the required update for tripal_feature when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>  7201 -   Fixes an error with the materialized view installation  
>  7202 -   Adds the temporary tables used for loading GFF files.
>
> tripal_views module :
>  7200 -   Tripal Views Update for 7.x-2.0    - Add relationship_only field to tripal_views_join    - Add relationship_handler field to tripal_views_join  
>
> tripal_pub module :
>  7202 -   Updates path of tripal_pub OBO to be relative.
>
> Performed update: tripal_feature_update_7200                                                    [ok]
> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
> does not exist
> LINE 3: tripal_mviews tm
>        ^
> Performed update: tripal_feature_update_7201                                                    [ok]
> Performed update: tripal_featuremap_update_7200                                                 [ok]
> Performed update: tripal_featuremap_update_7201                                                 [ok]
> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>
> Fatal error: Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
> Drush command terminated abnormally due to an unrecoverable error.                              [error]
> Error: Call to undefined function tripal_set_default_cv() in
> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
> The external command could not be executed due to an application error.                         [error]
> Finished performing updates.                                                                    [ok]
>
>
> ---------------------------------------------------------------------------------------------------------------------------------------------
> Full output after setting search_path to public, chado
>
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Stephen Ficklin-2
Hi Michael,

When you started your upgrade did you have the search_path set for the
postrgreSQL user?  (Step 3 in upgrade procedue
http://tripal.info/tutorials/v2.0/upgrade).  If so, then perhaps some of
the tables that should be in the 'public' schema in your D6 site are in
the 'chado' schema and they shouldn't be.   I do remember a bug at one
point in one of our development versions that caused this.  If this is
the case then it makes sense that you would have problems during the
upgrade.   Do you have a backup of your D6 site database where you can
look to see if those tables are in the 'chado' schema?  If so, moving
them to the 'public' schema and then retrying the upgrade may help.  If
you do see some of these tables in the 'chado' schema but you're unsure
if there are more that should also be moved feel free to send the list
of tables in your 'chado' schema and I can let you know.

Stephen

On 1/21/2016 1:15 AM, Michael Dondrup wrote:

> Hi,
> we fixed the first problem somehow the tripal_custom_tables table was created in chado schema. I moved it
> ALTER TABLE tripal_custom_tables SET SCHEMA public;
>
> Leaving me with this error:
>
> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>
>
> This is weird because the function is certainly defined in tripal/tripal_cv/api/tripal_cv.api.inc:function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE)
>
> I have tried to drush cc all and even rebuilt the registry as described here: https://www.drupal.org/project/registry_rebuild
>
> But to no avail. Anybody else having this problem?
>
> I really appreciate your help.
>
> Michael
>
>
>
>
> On Jan 20, 2016, at 2:17 PM, Michael Dondrup wrote:
>
>> Hi,
>>
>> we are doing a test-run of the D6->7 migration of our site including a Tripal update, following http://tripal.info/tutorials/v2.0/upgrade
>>
>> We are currently at step 14. Next, apply the Tripal updates: drush updatedb
>>
>> All core updates, views and ctools have been performed without error and no pending db updates were scheduled prior to this step.
>>
>>
>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>> does not exist
>> LINE 3: tripal_mviews tm
>>         ^
>>
>> [...]
>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>> Error: Call to undefined function tripal_set_default_cv() in
>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>> The external command could not be executed due to an application error.                         [error]
>>
>> I guess we have a fix for the first one, however that yields different errors:
>>
>> The table tripal_mviews exists but in the schema chado. I tried to set the search_path back:
>> ALTER USER user SET search_path TO public, chado;
>>
>> However this yields other errors:
>>
>> Cannot add field tripal_custom_tables.mview_id: table doesn't exist.                            [error]
>> [...]
>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install on line 449
>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>> Error: Call to undefined function tripal_insert_obo() in
>> /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install, line 449
>> The external command could not be executed due to an application error.                         [error]
>>
>>
>> I searched and found http://sourceforge.net/p/gmod/mailman/message/32762105/ but that doesn't seem to fit.
>>
>> Best
>>
>>
>>
>> Michael Dondrup
>> Researcher
>> Sea Lice Research Centre
>> Department of Informatics
>> University of Bergen
>> Thormøhlensgate 55, N-5008 Bergen,
>> Norway
>>
>>
>> Full output of drush updatedb first iteration:
>>
>> $ drush updatedb
>> The following updates are pending:
>>
>> tripal_core module :
>>   7200 -   Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table
>>   7201 -   Fixes missing language for nodes and URL aliases. This may take awhile...
>>   7202 -   Adds a tripal_token_formats table for custom page titles and URL paths
>>   7203 -   Adds a tripal_toc table for customizing the table of contents on each Tripal page.
>>   7204 -   Adds the tripal_variable_terms and a tripal_node_variables tables
>>
>> tripal_organism module :
>>   7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>
>> tripal_cv module :
>>   7201 -   Fixes an error with the materialized view installation
>>
>> tripal_contact module :
>>   7200 -   This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
>>   7201 -   Adds missing foreign key constraints
>>   7202 -   Updates path of tripal_contact OBO to be relative.
>>
>> tripal_bulk_loader module :
>>   7200 -   Implements hook_update_N().   Update to 7.x-2.0  -Cast tripal_bulk_loader.template_id to int field
>>
>> tripal_library module :
>>   7200 -   This is the required update for tripal_library when upgrading from Drupal core API 6.x.
>>   7201 -   Fixes an error with the materialized view installation
>>
>> tripal_stock module :
>>   7200 -   This is the required update for tripal_stock when upgrading from Drupal core API 6.x.
>>   7201 -   Add materialized views
>>
>> tripal_project module :
>>   7200 -   This is the required update for tripal_project when upgrading from Drupal core API 6.x.
>>
>> tripal_analysis module :
>>   7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>   7201 -   Fixes an error with the materialized view installation
>>
>> tripal_featuremap module :
>>   7200 -   This is the required update for tripal_featuremap when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>   7201 -   Adds missing foreign key constraints
>>   7202 -   Fixes a typo when setting the default CV for the unittype_id field of the featuremap table.
>>
>> tripal_feature module :
>>   7200 -   This is the required update for tripal_feature when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>   7201 -   Fixes an error with the materialized view installation
>>   7202 -   Adds the temporary tables used for loading GFF files.
>>
>> tripal_views module :
>>   7200 -   Tripal Views Update for 7.x-2.0    - Add relationship_only field to tripal_views_join    - Add relationship_handler field to tripal_views_join
>>
>> tripal_pub module :
>>   7202 -   Updates path of tripal_pub OBO to be relative.
>>
>> Performed update: tripal_feature_update_7200                                                    [ok]
>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>> does not exist
>> LINE 3: tripal_mviews tm
>>         ^
>> Performed update: tripal_feature_update_7201                                                    [ok]
>> Performed update: tripal_featuremap_update_7200                                                 [ok]
>> Performed update: tripal_featuremap_update_7201                                                 [ok]
>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>
>> Fatal error: Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>> Error: Call to undefined function tripal_set_default_cv() in
>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>> The external command could not be executed due to an application error.                         [error]
>> Finished performing updates.                                                                    [ok]
>>
>>
>> ---------------------------------------------------------------------------------------------------------------------------------------------
>> Full output after setting search_path to public, chado
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> _______________________________________________
>> Gmod-tripal mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Michael Dondrup-3
Hi Stephen,

thank your for your response, I think we are getting closer to the core of the problem.
Do you think this might cause also the 'call to undefined function' error?

Michael

On Jan 21, 2016, at 8:00 PM, Stephen Ficklin wrote:

> Hi Michael,
>
> When you started your upgrade did you have the search_path set for the postrgreSQL user?
Yes we had re-set the search path to public only.


>  (Step 3 in upgrade procedue http://tripal.info/tutorials/v2.0/upgrade).  If so, then perhaps some of the tables that should be in the 'public' schema in your D6 site are in the 'chado' schema and they shouldn't be.
I think this is the case: The following tripal* tables are in chado in our D6 system:

licebase=> \dt chado.tripal*
                List of relations
 Schema |         Name         | Type  |  Owner  
--------+----------------------+-------+----------
 chado  | tripal_custom_tables | table | lb_admin
 chado  | tripal_gff_temp      | table | lb_admin
 chado  | tripal_jobs          | table | lb_admin
 chado  | tripal_mviews        | table | lb_admin
 chado  | tripal_obo_temp      | table | lb_admin
(5 rows)

The following ones are in public

licebase=> \dt public.tripal*
                    List of relations
 Schema |             Name             | Type  |  Owner  
--------+------------------------------+-------+----------
 public | tripal_analysis              | table | lb_admin
 public | tripal_analysis_blast        | table | lb_admin
 public | tripal_bulk_loader           | table | lb_admin
 public | tripal_bulk_loader_constants | table | lb_admin
 public | tripal_bulk_loader_inserted  | table | lb_admin
 public | tripal_bulk_loader_template  | table | lb_admin
 public | tripal_cv_obo                | table | lb_admin
 public | tripal_feature_relagg        | table | lb_admin
 public | tripal_pub_import            | table | lb_admin
 public | tripal_views                 | table | lb_admin
 public | tripal_views_field           | table | lb_admin
 public | tripal_views_handlers        | table | lb_admin
 public | tripal_views_join            | table | lb_admin
(13 rows)




>   I do remember a bug at one point in one of our development versions that caused this.  If this is the case then it makes sense that you would have problems during the upgrade.   Do you have a backup of your D6 site database where you can look to see if those tables are in the 'chado' schema?
W are working on an identical copy, while the D6 Tripal1 system is still online and we have backups of each stage so we can start over. So I could just look it up in the
production system.


>  If so, moving them to the 'public' schema and then retrying the upgrade may help.  If you do see some of these tables in the 'chado' schema but you're unsure if there are more that should also be moved feel free to send the list of tables in your 'chado' schema and I can let you know.
So should I first attempt move all those tripal* tables from chado to public? Funny enough this doesn't cause problems in the D6 system....


>
> Stephen
>
> On 1/21/2016 1:15 AM, Michael Dondrup wrote:
>> Hi,
>> we fixed the first problem somehow the tripal_custom_tables table was created in chado schema. I moved it
>> ALTER TABLE tripal_custom_tables SET SCHEMA public;
>>
>> Leaving me with this error:
>>
>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>
>>
>> This is weird because the function is certainly defined in tripal/tripal_cv/api/tripal_cv.api.inc:function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE)
>>
>> I have tried to drush cc all and even rebuilt the registry as described here: https://www.drupal.org/project/registry_rebuild
>>
>> But to no avail. Anybody else having this problem?
>>
>> I really appreciate your help.
>>
>> Michael
>>
>>
>>
>>
>> On Jan 20, 2016, at 2:17 PM, Michael Dondrup wrote:
>>
>>> Hi,
>>>
>>> we are doing a test-run of the D6->7 migration of our site including a Tripal update, following http://tripal.info/tutorials/v2.0/upgrade
>>>
>>> We are currently at step 14. Next, apply the Tripal updates: drush updatedb
>>>
>>> All core updates, views and ctools have been performed without error and no pending db updates were scheduled prior to this step.
>>>
>>>
>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>> does not exist
>>> LINE 3: tripal_mviews tm
>>>        ^
>>>
>>> [...]
>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>> Error: Call to undefined function tripal_set_default_cv() in
>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>> The external command could not be executed due to an application error.                         [error]
>>>
>>> I guess we have a fix for the first one, however that yields different errors:
>>>
>>> The table tripal_mviews exists but in the schema chado. I tried to set the search_path back:
>>> ALTER USER user SET search_path TO public, chado;
>>>
>>> However this yields other errors:
>>>
>>> Cannot add field tripal_custom_tables.mview_id: table doesn't exist.                            [error]
>>> [...]
>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install on line 449
>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>> Error: Call to undefined function tripal_insert_obo() in
>>> /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install, line 449
>>> The external command could not be executed due to an application error.                         [error]
>>>
>>>
>>> I searched and found http://sourceforge.net/p/gmod/mailman/message/32762105/ but that doesn't seem to fit.
>>>
>>> Best
>>>
>>>
>>>
>>> Michael Dondrup
>>> Researcher
>>> Sea Lice Research Centre
>>> Department of Informatics
>>> University of Bergen
>>> Thormøhlensgate 55, N-5008 Bergen,
>>> Norway
>>>
>>>
>>> Full output of drush updatedb first iteration:
>>>
>>> $ drush updatedb
>>> The following updates are pending:
>>>
>>> tripal_core module :
>>>  7200 -   Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table
>>>  7201 -   Fixes missing language for nodes and URL aliases. This may take awhile...
>>>  7202 -   Adds a tripal_token_formats table for custom page titles and URL paths
>>>  7203 -   Adds a tripal_toc table for customizing the table of contents on each Tripal page.
>>>  7204 -   Adds the tripal_variable_terms and a tripal_node_variables tables
>>>
>>> tripal_organism module :
>>>  7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>
>>> tripal_cv module :
>>>  7201 -   Fixes an error with the materialized view installation
>>>
>>> tripal_contact module :
>>>  7200 -   This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
>>>  7201 -   Adds missing foreign key constraints
>>>  7202 -   Updates path of tripal_contact OBO to be relative.
>>>
>>> tripal_bulk_loader module :
>>>  7200 -   Implements hook_update_N().   Update to 7.x-2.0  -Cast tripal_bulk_loader.template_id to int field
>>>
>>> tripal_library module :
>>>  7200 -   This is the required update for tripal_library when upgrading from Drupal core API 6.x.
>>>  7201 -   Fixes an error with the materialized view installation
>>>
>>> tripal_stock module :
>>>  7200 -   This is the required update for tripal_stock when upgrading from Drupal core API 6.x.
>>>  7201 -   Add materialized views
>>>
>>> tripal_project module :
>>>  7200 -   This is the required update for tripal_project when upgrading from Drupal core API 6.x.
>>>
>>> tripal_analysis module :
>>>  7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>  7201 -   Fixes an error with the materialized view installation
>>>
>>> tripal_featuremap module :
>>>  7200 -   This is the required update for tripal_featuremap when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>  7201 -   Adds missing foreign key constraints
>>>  7202 -   Fixes a typo when setting the default CV for the unittype_id field of the featuremap table.
>>>
>>> tripal_feature module :
>>>  7200 -   This is the required update for tripal_feature when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>  7201 -   Fixes an error with the materialized view installation
>>>  7202 -   Adds the temporary tables used for loading GFF files.
>>>
>>> tripal_views module :
>>>  7200 -   Tripal Views Update for 7.x-2.0    - Add relationship_only field to tripal_views_join    - Add relationship_handler field to tripal_views_join
>>>
>>> tripal_pub module :
>>>  7202 -   Updates path of tripal_pub OBO to be relative.
>>>
>>> Performed update: tripal_feature_update_7200                                                    [ok]
>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>> does not exist
>>> LINE 3: tripal_mviews tm
>>>        ^
>>> Performed update: tripal_feature_update_7201                                                    [ok]
>>> Performed update: tripal_featuremap_update_7200                                                 [ok]
>>> Performed update: tripal_featuremap_update_7201                                                 [ok]
>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>
>>> Fatal error: Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>> Error: Call to undefined function tripal_set_default_cv() in
>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>> The external command could not be executed due to an application error.                         [error]
>>> Finished performing updates.                                                                    [ok]
>>>
>>>
>>> ---------------------------------------------------------------------------------------------------------------------------------------------
>>> Full output after setting search_path to public, chado
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>> _______________________________________________
>>> Gmod-tripal mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> _______________________________________________
>> Gmod-tripal mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Michael Dondrup-3
Hi,
we are still getting the 'undefined function errors' for functions that are in reality defined in the code of tripal:
e.g. tripal_add_mview() or tripal_insert_obo(). These functions sometimes change erratically throughout the process.
We were suspecting the drush version as we were initially using drush 5.7, we have therefore tested with other
versions: 6.4 (as recommended in the documentation), 6.0, 6.7 (latest stable 6), 5.5.9. We also tried drush 7 branches, but
these don't recognize a drupal site.

Drush install via composer, php version is PHP 5.3.3

Each time we cleared the cache (drush cc all) and rebuilt the drush registry (drush rr). To no avail. As the process is a bit erratic
I interpret this as caused by the sequence of php file inclusions.  

We have certainly hit a wall here, and would appreciate any input as the migration is somewhat urgent to cmplete.

Thank you in advance for your help.

Michael
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Full output below:

$ drush updb
 Tripal_core        7204  Adds the tripal_variable_terms and a tripal_node_variables tables        
 Tripal_feature     7202  Adds the temporary tables used for loading GFF files.                    
 Tripal_pub         7202  Updates path of tripal_pub OBO to be relative.                            
 Tripal_stock       7201  Add materialized views                                                    
 Tripal_contact     7202  Updates path of tripal_contact OBO to be relative.                        
 Tripal_featuremap  7202  Fixes a typo when setting the default CV for the unittype_id field of the
                          featuremap table.
Do you wish to run all pending updates? (y/n): y
PHP Fatal error:  Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409

Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
Drush command terminated abnormally due to an unrecoverable error.                              [error]
Error: Call to undefined function tripal_insert_obo() in
/home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install, line 409
The external command could not be executed due to an application error.                         [error]
'all' cache was cleared in self                                                                 [success]
Finished performing updates.                                                                    [ok]








On Jan 21, 2016, at 9:32 PM, Michael Dondrup wrote:

> Hi Stephen,
>
> thank your for your response, I think we are getting closer to the core of the problem.
> Do you think this might cause also the 'call to undefined function' error?
>
> Michael
>
> On Jan 21, 2016, at 8:00 PM, Stephen Ficklin wrote:
>
>> Hi Michael,
>>
>> When you started your upgrade did you have the search_path set for the postrgreSQL user?
> Yes we had re-set the search path to public only.
>
>
>> (Step 3 in upgrade procedue http://tripal.info/tutorials/v2.0/upgrade).  If so, then perhaps some of the tables that should be in the 'public' schema in your D6 site are in the 'chado' schema and they shouldn't be.
> I think this is the case: The following tripal* tables are in chado in our D6 system:
>
> licebase=> \dt chado.tripal*
>                List of relations
> Schema |         Name         | Type  |  Owner  
> --------+----------------------+-------+----------
> chado  | tripal_custom_tables | table | lb_admin
> chado  | tripal_gff_temp      | table | lb_admin
> chado  | tripal_jobs          | table | lb_admin
> chado  | tripal_mviews        | table | lb_admin
> chado  | tripal_obo_temp      | table | lb_admin
> (5 rows)
>
> The following ones are in public
>
> licebase=> \dt public.tripal*
>                    List of relations
> Schema |             Name             | Type  |  Owner  
> --------+------------------------------+-------+----------
> public | tripal_analysis              | table | lb_admin
> public | tripal_analysis_blast        | table | lb_admin
> public | tripal_bulk_loader           | table | lb_admin
> public | tripal_bulk_loader_constants | table | lb_admin
> public | tripal_bulk_loader_inserted  | table | lb_admin
> public | tripal_bulk_loader_template  | table | lb_admin
> public | tripal_cv_obo                | table | lb_admin
> public | tripal_feature_relagg        | table | lb_admin
> public | tripal_pub_import            | table | lb_admin
> public | tripal_views                 | table | lb_admin
> public | tripal_views_field           | table | lb_admin
> public | tripal_views_handlers        | table | lb_admin
> public | tripal_views_join            | table | lb_admin
> (13 rows)
>
>
>
>
>>  I do remember a bug at one point in one of our development versions that caused this.  If this is the case then it makes sense that you would have problems during the upgrade.   Do you have a backup of your D6 site database where you can look to see if those tables are in the 'chado' schema?
> W are working on an identical copy, while the D6 Tripal1 system is still online and we have backups of each stage so we can start over. So I could just look it up in the
> production system.
>
>
>> If so, moving them to the 'public' schema and then retrying the upgrade may help.  If you do see some of these tables in the 'chado' schema but you're unsure if there are more that should also be moved feel free to send the list of tables in your 'chado' schema and I can let you know.
> So should I first attempt move all those tripal* tables from chado to public? Funny enough this doesn't cause problems in the D6 system....
>
>
>>
>> Stephen
>>
>> On 1/21/2016 1:15 AM, Michael Dondrup wrote:
>>> Hi,
>>> we fixed the first problem somehow the tripal_custom_tables table was created in chado schema. I moved it
>>> ALTER TABLE tripal_custom_tables SET SCHEMA public;
>>>
>>> Leaving me with this error:
>>>
>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>
>>>
>>> This is weird because the function is certainly defined in tripal/tripal_cv/api/tripal_cv.api.inc:function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE)
>>>
>>> I have tried to drush cc all and even rebuilt the registry as described here: https://www.drupal.org/project/registry_rebuild
>>>
>>> But to no avail. Anybody else having this problem?
>>>
>>> I really appreciate your help.
>>>
>>> Michael
>>>
>>>
>>>
>>>
>>> On Jan 20, 2016, at 2:17 PM, Michael Dondrup wrote:
>>>
>>>> Hi,
>>>>
>>>> we are doing a test-run of the D6->7 migration of our site including a Tripal update, following http://tripal.info/tutorials/v2.0/upgrade
>>>>
>>>> We are currently at step 14. Next, apply the Tripal updates: drush updatedb
>>>>
>>>> All core updates, views and ctools have been performed without error and no pending db updates were scheduled prior to this step.
>>>>
>>>>
>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>> does not exist
>>>> LINE 3: tripal_mviews tm
>>>>       ^
>>>>
>>>> [...]
>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>> The external command could not be executed due to an application error.                         [error]
>>>>
>>>> I guess we have a fix for the first one, however that yields different errors:
>>>>
>>>> The table tripal_mviews exists but in the schema chado. I tried to set the search_path back:
>>>> ALTER USER user SET search_path TO public, chado;
>>>>
>>>> However this yields other errors:
>>>>
>>>> Cannot add field tripal_custom_tables.mview_id: table doesn't exist.                            [error]
>>>> [...]
>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install on line 449
>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>> Error: Call to undefined function tripal_insert_obo() in
>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install, line 449
>>>> The external command could not be executed due to an application error.                         [error]
>>>>
>>>>
>>>> I searched and found http://sourceforge.net/p/gmod/mailman/message/32762105/ but that doesn't seem to fit.
>>>>
>>>> Best
>>>>
>>>>
>>>>
>>>> Michael Dondrup
>>>> Researcher
>>>> Sea Lice Research Centre
>>>> Department of Informatics
>>>> University of Bergen
>>>> Thormøhlensgate 55, N-5008 Bergen,
>>>> Norway
>>>>
>>>>
>>>> Full output of drush updatedb first iteration:
>>>>
>>>> $ drush updatedb
>>>> The following updates are pending:
>>>>
>>>> tripal_core module :
>>>> 7200 -   Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table
>>>> 7201 -   Fixes missing language for nodes and URL aliases. This may take awhile...
>>>> 7202 -   Adds a tripal_token_formats table for custom page titles and URL paths
>>>> 7203 -   Adds a tripal_toc table for customizing the table of contents on each Tripal page.
>>>> 7204 -   Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>
>>>> tripal_organism module :
>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>
>>>> tripal_cv module :
>>>> 7201 -   Fixes an error with the materialized view installation
>>>>
>>>> tripal_contact module :
>>>> 7200 -   This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
>>>> 7201 -   Adds missing foreign key constraints
>>>> 7202 -   Updates path of tripal_contact OBO to be relative.
>>>>
>>>> tripal_bulk_loader module :
>>>> 7200 -   Implements hook_update_N().   Update to 7.x-2.0  -Cast tripal_bulk_loader.template_id to int field
>>>>
>>>> tripal_library module :
>>>> 7200 -   This is the required update for tripal_library when upgrading from Drupal core API 6.x.
>>>> 7201 -   Fixes an error with the materialized view installation
>>>>
>>>> tripal_stock module :
>>>> 7200 -   This is the required update for tripal_stock when upgrading from Drupal core API 6.x.
>>>> 7201 -   Add materialized views
>>>>
>>>> tripal_project module :
>>>> 7200 -   This is the required update for tripal_project when upgrading from Drupal core API 6.x.
>>>>
>>>> tripal_analysis module :
>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>> 7201 -   Fixes an error with the materialized view installation
>>>>
>>>> tripal_featuremap module :
>>>> 7200 -   This is the required update for tripal_featuremap when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>> 7201 -   Adds missing foreign key constraints
>>>> 7202 -   Fixes a typo when setting the default CV for the unittype_id field of the featuremap table.
>>>>
>>>> tripal_feature module :
>>>> 7200 -   This is the required update for tripal_feature when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>> 7201 -   Fixes an error with the materialized view installation
>>>> 7202 -   Adds the temporary tables used for loading GFF files.
>>>>
>>>> tripal_views module :
>>>> 7200 -   Tripal Views Update for 7.x-2.0    - Add relationship_only field to tripal_views_join    - Add relationship_handler field to tripal_views_join
>>>>
>>>> tripal_pub module :
>>>> 7202 -   Updates path of tripal_pub OBO to be relative.
>>>>
>>>> Performed update: tripal_feature_update_7200                                                    [ok]
>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>> does not exist
>>>> LINE 3: tripal_mviews tm
>>>>       ^
>>>> Performed update: tripal_feature_update_7201                                                    [ok]
>>>> Performed update: tripal_featuremap_update_7200                                                 [ok]
>>>> Performed update: tripal_featuremap_update_7201                                                 [ok]
>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>
>>>> Fatal error: Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>> The external command could not be executed due to an application error.                         [error]
>>>> Finished performing updates.                                                                    [ok]
>>>>
>>>>
>>>> ---------------------------------------------------------------------------------------------------------------------------------------------
>>>> Full output after setting search_path to public, chado
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>> Monitor end-to-end web transactions and take corrective actions now
>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>> _______________________________________________
>>>> Gmod-tripal mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>> _______________________________________________
>>> Gmod-tripal mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Stephen Ficklin-2
Hi Michael,

I believe I understand what the problem is.   I'm going to add a fix to
Tripal v2.x (the development branch) and let you know when it's ready.  
Can you use the development branch for testing your upgrade?  We're very
close to releasing v2.1 so it should be stable enough to use.

Stephen

On 1/22/2016 2:39 AM, Michael Dondrup wrote:

> Hi,
> we are still getting the 'undefined function errors' for functions that are in reality defined in the code of tripal:
> e.g. tripal_add_mview() or tripal_insert_obo(). These functions sometimes change erratically throughout the process.
> We were suspecting the drush version as we were initially using drush 5.7, we have therefore tested with other
> versions: 6.4 (as recommended in the documentation), 6.0, 6.7 (latest stable 6), 5.5.9. We also tried drush 7 branches, but
> these don't recognize a drupal site.
>
> Drush install via composer, php version is PHP 5.3.3
>
> Each time we cleared the cache (drush cc all) and rebuilt the drush registry (drush rr). To no avail. As the process is a bit erratic
> I interpret this as caused by the sequence of php file inclusions.
>
> We have certainly hit a wall here, and would appreciate any input as the migration is somewhat urgent to cmplete.
>
> Thank you in advance for your help.
>
> Michael
> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> Full output below:
>
> $ drush updb
>   Tripal_core        7204  Adds the tripal_variable_terms and a tripal_node_variables tables
>   Tripal_feature     7202  Adds the temporary tables used for loading GFF files.
>   Tripal_pub         7202  Updates path of tripal_pub OBO to be relative.
>   Tripal_stock       7201  Add materialized views
>   Tripal_contact     7202  Updates path of tripal_contact OBO to be relative.
>   Tripal_featuremap  7202  Fixes a typo when setting the default CV for the unittype_id field of the
>                            featuremap table.
> Do you wish to run all pending updates? (y/n): y
> PHP Fatal error:  Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>
> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
> Drush command terminated abnormally due to an unrecoverable error.                              [error]
> Error: Call to undefined function tripal_insert_obo() in
> /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install, line 409
> The external command could not be executed due to an application error.                         [error]
> 'all' cache was cleared in self                                                                 [success]
> Finished performing updates.                                                                    [ok]
>
>
>
>
>
>
>
>
> On Jan 21, 2016, at 9:32 PM, Michael Dondrup wrote:
>
>> Hi Stephen,
>>
>> thank your for your response, I think we are getting closer to the core of the problem.
>> Do you think this might cause also the 'call to undefined function' error?
>>
>> Michael
>>
>> On Jan 21, 2016, at 8:00 PM, Stephen Ficklin wrote:
>>
>>> Hi Michael,
>>>
>>> When you started your upgrade did you have the search_path set for the postrgreSQL user?
>> Yes we had re-set the search path to public only.
>>
>>
>>> (Step 3 in upgrade procedue http://tripal.info/tutorials/v2.0/upgrade).  If so, then perhaps some of the tables that should be in the 'public' schema in your D6 site are in the 'chado' schema and they shouldn't be.
>> I think this is the case: The following tripal* tables are in chado in our D6 system:
>>
>> licebase=> \dt chado.tripal*
>>                 List of relations
>> Schema |         Name         | Type  |  Owner
>> --------+----------------------+-------+----------
>> chado  | tripal_custom_tables | table | lb_admin
>> chado  | tripal_gff_temp      | table | lb_admin
>> chado  | tripal_jobs          | table | lb_admin
>> chado  | tripal_mviews        | table | lb_admin
>> chado  | tripal_obo_temp      | table | lb_admin
>> (5 rows)
>>
>> The following ones are in public
>>
>> licebase=> \dt public.tripal*
>>                     List of relations
>> Schema |             Name             | Type  |  Owner
>> --------+------------------------------+-------+----------
>> public | tripal_analysis              | table | lb_admin
>> public | tripal_analysis_blast        | table | lb_admin
>> public | tripal_bulk_loader           | table | lb_admin
>> public | tripal_bulk_loader_constants | table | lb_admin
>> public | tripal_bulk_loader_inserted  | table | lb_admin
>> public | tripal_bulk_loader_template  | table | lb_admin
>> public | tripal_cv_obo                | table | lb_admin
>> public | tripal_feature_relagg        | table | lb_admin
>> public | tripal_pub_import            | table | lb_admin
>> public | tripal_views                 | table | lb_admin
>> public | tripal_views_field           | table | lb_admin
>> public | tripal_views_handlers        | table | lb_admin
>> public | tripal_views_join            | table | lb_admin
>> (13 rows)
>>
>>
>>
>>
>>>   I do remember a bug at one point in one of our development versions that caused this.  If this is the case then it makes sense that you would have problems during the upgrade.   Do you have a backup of your D6 site database where you can look to see if those tables are in the 'chado' schema?
>> W are working on an identical copy, while the D6 Tripal1 system is still online and we have backups of each stage so we can start over. So I could just look it up in the
>> production system.
>>
>>
>>> If so, moving them to the 'public' schema and then retrying the upgrade may help.  If you do see some of these tables in the 'chado' schema but you're unsure if there are more that should also be moved feel free to send the list of tables in your 'chado' schema and I can let you know.
>> So should I first attempt move all those tripal* tables from chado to public? Funny enough this doesn't cause problems in the D6 system....
>>
>>
>>> Stephen
>>>
>>> On 1/21/2016 1:15 AM, Michael Dondrup wrote:
>>>> Hi,
>>>> we fixed the first problem somehow the tripal_custom_tables table was created in chado schema. I moved it
>>>> ALTER TABLE tripal_custom_tables SET SCHEMA public;
>>>>
>>>> Leaving me with this error:
>>>>
>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>
>>>>
>>>> This is weird because the function is certainly defined in tripal/tripal_cv/api/tripal_cv.api.inc:function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE)
>>>>
>>>> I have tried to drush cc all and even rebuilt the registry as described here: https://www.drupal.org/project/registry_rebuild
>>>>
>>>> But to no avail. Anybody else having this problem?
>>>>
>>>> I really appreciate your help.
>>>>
>>>> Michael
>>>>
>>>>
>>>>
>>>>
>>>> On Jan 20, 2016, at 2:17 PM, Michael Dondrup wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> we are doing a test-run of the D6->7 migration of our site including a Tripal update, following http://tripal.info/tutorials/v2.0/upgrade
>>>>>
>>>>> We are currently at step 14. Next, apply the Tripal updates: drush updatedb
>>>>>
>>>>> All core updates, views and ctools have been performed without error and no pending db updates were scheduled prior to this step.
>>>>>
>>>>>
>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>> does not exist
>>>>> LINE 3: tripal_mviews tm
>>>>>        ^
>>>>>
>>>>> [...]
>>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>
>>>>> I guess we have a fix for the first one, however that yields different errors:
>>>>>
>>>>> The table tripal_mviews exists but in the schema chado. I tried to set the search_path back:
>>>>> ALTER USER user SET search_path TO public, chado;
>>>>>
>>>>> However this yields other errors:
>>>>>
>>>>> Cannot add field tripal_custom_tables.mview_id: table doesn't exist.                            [error]
>>>>> [...]
>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install on line 449
>>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install, line 449
>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>
>>>>>
>>>>> I searched and found http://sourceforge.net/p/gmod/mailman/message/32762105/ but that doesn't seem to fit.
>>>>>
>>>>> Best
>>>>>
>>>>>
>>>>>
>>>>> Michael Dondrup
>>>>> Researcher
>>>>> Sea Lice Research Centre
>>>>> Department of Informatics
>>>>> University of Bergen
>>>>> Thormøhlensgate 55, N-5008 Bergen,
>>>>> Norway
>>>>>
>>>>>
>>>>> Full output of drush updatedb first iteration:
>>>>>
>>>>> $ drush updatedb
>>>>> The following updates are pending:
>>>>>
>>>>> tripal_core module :
>>>>> 7200 -   Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table
>>>>> 7201 -   Fixes missing language for nodes and URL aliases. This may take awhile...
>>>>> 7202 -   Adds a tripal_token_formats table for custom page titles and URL paths
>>>>> 7203 -   Adds a tripal_toc table for customizing the table of contents on each Tripal page.
>>>>> 7204 -   Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>
>>>>> tripal_organism module :
>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>
>>>>> tripal_cv module :
>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>
>>>>> tripal_contact module :
>>>>> 7200 -   This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
>>>>> 7201 -   Adds missing foreign key constraints
>>>>> 7202 -   Updates path of tripal_contact OBO to be relative.
>>>>>
>>>>> tripal_bulk_loader module :
>>>>> 7200 -   Implements hook_update_N().   Update to 7.x-2.0  -Cast tripal_bulk_loader.template_id to int field
>>>>>
>>>>> tripal_library module :
>>>>> 7200 -   This is the required update for tripal_library when upgrading from Drupal core API 6.x.
>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>
>>>>> tripal_stock module :
>>>>> 7200 -   This is the required update for tripal_stock when upgrading from Drupal core API 6.x.
>>>>> 7201 -   Add materialized views
>>>>>
>>>>> tripal_project module :
>>>>> 7200 -   This is the required update for tripal_project when upgrading from Drupal core API 6.x.
>>>>>
>>>>> tripal_analysis module :
>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>
>>>>> tripal_featuremap module :
>>>>> 7200 -   This is the required update for tripal_featuremap when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>> 7201 -   Adds missing foreign key constraints
>>>>> 7202 -   Fixes a typo when setting the default CV for the unittype_id field of the featuremap table.
>>>>>
>>>>> tripal_feature module :
>>>>> 7200 -   This is the required update for tripal_feature when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>> 7202 -   Adds the temporary tables used for loading GFF files.
>>>>>
>>>>> tripal_views module :
>>>>> 7200 -   Tripal Views Update for 7.x-2.0    - Add relationship_only field to tripal_views_join    - Add relationship_handler field to tripal_views_join
>>>>>
>>>>> tripal_pub module :
>>>>> 7202 -   Updates path of tripal_pub OBO to be relative.
>>>>>
>>>>> Performed update: tripal_feature_update_7200                                                    [ok]
>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>> does not exist
>>>>> LINE 3: tripal_mviews tm
>>>>>        ^
>>>>> Performed update: tripal_feature_update_7201                                                    [ok]
>>>>> Performed update: tripal_featuremap_update_7200                                                 [ok]
>>>>> Performed update: tripal_featuremap_update_7201                                                 [ok]
>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>
>>>>> Fatal error: Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>> The external command could not be executed due to an application error.                         [error]
>>>>> Finished performing updates.                                                                    [ok]
>>>>>
>>>>>
>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------
>>>>> Full output after setting search_path to public, chado
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>> _______________________________________________
>>>>> Gmod-tripal mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>> ------------------------------------------------------------------------------
>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>> Monitor end-to-end web transactions and take corrective actions now
>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>> _______________________________________________
>>>> Gmod-tripal mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> _______________________________________________
>> Gmod-tripal mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Michael Dondrup-3
Hi Stephen,

That would be great, we will just revert to the state directly after updating clean drupal core
next week.
Will php 5.3.3 and drush 6.7.0 be ok?

Michael


On Jan 22, 2016, at 6:31 PM, Stephen Ficklin wrote:

> Hi Michael,
>
> I believe I understand what the problem is.   I'm going to add a fix to Tripal v2.x (the development branch) and let you know when it's ready.  Can you use the development branch for testing your upgrade?  We're very close to releasing v2.1 so it should be stable enough to use.
>
> Stephen
>
> On 1/22/2016 2:39 AM, Michael Dondrup wrote:
>> Hi,
>> we are still getting the 'undefined function errors' for functions that are in reality defined in the code of tripal:
>> e.g. tripal_add_mview() or tripal_insert_obo(). These functions sometimes change erratically throughout the process.
>> We were suspecting the drush version as we were initially using drush 5.7, we have therefore tested with other
>> versions: 6.4 (as recommended in the documentation), 6.0, 6.7 (latest stable 6), 5.5.9. We also tried drush 7 branches, but
>> these don't recognize a drupal site.
>>
>> Drush install via composer, php version is PHP 5.3.3
>>
>> Each time we cleared the cache (drush cc all) and rebuilt the drush registry (drush rr). To no avail. As the process is a bit erratic
>> I interpret this as caused by the sequence of php file inclusions.
>>
>> We have certainly hit a wall here, and would appreciate any input as the migration is somewhat urgent to cmplete.
>>
>> Thank you in advance for your help.
>>
>> Michael
>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>> Full output below:
>>
>> $ drush updb
>>  Tripal_core        7204  Adds the tripal_variable_terms and a tripal_node_variables tables
>>  Tripal_feature     7202  Adds the temporary tables used for loading GFF files.
>>  Tripal_pub         7202  Updates path of tripal_pub OBO to be relative.
>>  Tripal_stock       7201  Add materialized views
>>  Tripal_contact     7202  Updates path of tripal_contact OBO to be relative.
>>  Tripal_featuremap  7202  Fixes a typo when setting the default CV for the unittype_id field of the
>>                           featuremap table.
>> Do you wish to run all pending updates? (y/n): y
>> PHP Fatal error:  Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>
>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>> Error: Call to undefined function tripal_insert_obo() in
>> /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install, line 409
>> The external command could not be executed due to an application error.                         [error]
>> 'all' cache was cleared in self                                                                 [success]
>> Finished performing updates.                                                                    [ok]
>>
>>
>>
>>
>>
>>
>>
>>
>> On Jan 21, 2016, at 9:32 PM, Michael Dondrup wrote:
>>
>>> Hi Stephen,
>>>
>>> thank your for your response, I think we are getting closer to the core of the problem.
>>> Do you think this might cause also the 'call to undefined function' error?
>>>
>>> Michael
>>>
>>> On Jan 21, 2016, at 8:00 PM, Stephen Ficklin wrote:
>>>
>>>> Hi Michael,
>>>>
>>>> When you started your upgrade did you have the search_path set for the postrgreSQL user?
>>> Yes we had re-set the search path to public only.
>>>
>>>
>>>> (Step 3 in upgrade procedue http://tripal.info/tutorials/v2.0/upgrade).  If so, then perhaps some of the tables that should be in the 'public' schema in your D6 site are in the 'chado' schema and they shouldn't be.
>>> I think this is the case: The following tripal* tables are in chado in our D6 system:
>>>
>>> licebase=> \dt chado.tripal*
>>>                List of relations
>>> Schema |         Name         | Type  |  Owner
>>> --------+----------------------+-------+----------
>>> chado  | tripal_custom_tables | table | lb_admin
>>> chado  | tripal_gff_temp      | table | lb_admin
>>> chado  | tripal_jobs          | table | lb_admin
>>> chado  | tripal_mviews        | table | lb_admin
>>> chado  | tripal_obo_temp      | table | lb_admin
>>> (5 rows)
>>>
>>> The following ones are in public
>>>
>>> licebase=> \dt public.tripal*
>>>                    List of relations
>>> Schema |             Name             | Type  |  Owner
>>> --------+------------------------------+-------+----------
>>> public | tripal_analysis              | table | lb_admin
>>> public | tripal_analysis_blast        | table | lb_admin
>>> public | tripal_bulk_loader           | table | lb_admin
>>> public | tripal_bulk_loader_constants | table | lb_admin
>>> public | tripal_bulk_loader_inserted  | table | lb_admin
>>> public | tripal_bulk_loader_template  | table | lb_admin
>>> public | tripal_cv_obo                | table | lb_admin
>>> public | tripal_feature_relagg        | table | lb_admin
>>> public | tripal_pub_import            | table | lb_admin
>>> public | tripal_views                 | table | lb_admin
>>> public | tripal_views_field           | table | lb_admin
>>> public | tripal_views_handlers        | table | lb_admin
>>> public | tripal_views_join            | table | lb_admin
>>> (13 rows)
>>>
>>>
>>>
>>>
>>>>  I do remember a bug at one point in one of our development versions that caused this.  If this is the case then it makes sense that you would have problems during the upgrade.   Do you have a backup of your D6 site database where you can look to see if those tables are in the 'chado' schema?
>>> W are working on an identical copy, while the D6 Tripal1 system is still online and we have backups of each stage so we can start over. So I could just look it up in the
>>> production system.
>>>
>>>
>>>> If so, moving them to the 'public' schema and then retrying the upgrade may help.  If you do see some of these tables in the 'chado' schema but you're unsure if there are more that should also be moved feel free to send the list of tables in your 'chado' schema and I can let you know.
>>> So should I first attempt move all those tripal* tables from chado to public? Funny enough this doesn't cause problems in the D6 system....
>>>
>>>
>>>> Stephen
>>>>
>>>> On 1/21/2016 1:15 AM, Michael Dondrup wrote:
>>>>> Hi,
>>>>> we fixed the first problem somehow the tripal_custom_tables table was created in chado schema. I moved it
>>>>> ALTER TABLE tripal_custom_tables SET SCHEMA public;
>>>>>
>>>>> Leaving me with this error:
>>>>>
>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>
>>>>>
>>>>> This is weird because the function is certainly defined in tripal/tripal_cv/api/tripal_cv.api.inc:function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE)
>>>>>
>>>>> I have tried to drush cc all and even rebuilt the registry as described here: https://www.drupal.org/project/registry_rebuild
>>>>>
>>>>> But to no avail. Anybody else having this problem?
>>>>>
>>>>> I really appreciate your help.
>>>>>
>>>>> Michael
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Jan 20, 2016, at 2:17 PM, Michael Dondrup wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> we are doing a test-run of the D6->7 migration of our site including a Tripal update, following http://tripal.info/tutorials/v2.0/upgrade
>>>>>>
>>>>>> We are currently at step 14. Next, apply the Tripal updates: drush updatedb
>>>>>>
>>>>>> All core updates, views and ctools have been performed without error and no pending db updates were scheduled prior to this step.
>>>>>>
>>>>>>
>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>> does not exist
>>>>>> LINE 3: tripal_mviews tm
>>>>>>       ^
>>>>>>
>>>>>> [...]
>>>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>
>>>>>> I guess we have a fix for the first one, however that yields different errors:
>>>>>>
>>>>>> The table tripal_mviews exists but in the schema chado. I tried to set the search_path back:
>>>>>> ALTER USER user SET search_path TO public, chado;
>>>>>>
>>>>>> However this yields other errors:
>>>>>>
>>>>>> Cannot add field tripal_custom_tables.mview_id: table doesn't exist.                            [error]
>>>>>> [...]
>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install on line 449
>>>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install, line 449
>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>
>>>>>>
>>>>>> I searched and found http://sourceforge.net/p/gmod/mailman/message/32762105/ but that doesn't seem to fit.
>>>>>>
>>>>>> Best
>>>>>>
>>>>>>
>>>>>>
>>>>>> Michael Dondrup
>>>>>> Researcher
>>>>>> Sea Lice Research Centre
>>>>>> Department of Informatics
>>>>>> University of Bergen
>>>>>> Thormøhlensgate 55, N-5008 Bergen,
>>>>>> Norway
>>>>>>
>>>>>>
>>>>>> Full output of drush updatedb first iteration:
>>>>>>
>>>>>> $ drush updatedb
>>>>>> The following updates are pending:
>>>>>>
>>>>>> tripal_core module :
>>>>>> 7200 -   Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table
>>>>>> 7201 -   Fixes missing language for nodes and URL aliases. This may take awhile...
>>>>>> 7202 -   Adds a tripal_token_formats table for custom page titles and URL paths
>>>>>> 7203 -   Adds a tripal_toc table for customizing the table of contents on each Tripal page.
>>>>>> 7204 -   Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>
>>>>>> tripal_organism module :
>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>
>>>>>> tripal_cv module :
>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>
>>>>>> tripal_contact module :
>>>>>> 7200 -   This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>> 7202 -   Updates path of tripal_contact OBO to be relative.
>>>>>>
>>>>>> tripal_bulk_loader module :
>>>>>> 7200 -   Implements hook_update_N().   Update to 7.x-2.0  -Cast tripal_bulk_loader.template_id to int field
>>>>>>
>>>>>> tripal_library module :
>>>>>> 7200 -   This is the required update for tripal_library when upgrading from Drupal core API 6.x.
>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>
>>>>>> tripal_stock module :
>>>>>> 7200 -   This is the required update for tripal_stock when upgrading from Drupal core API 6.x.
>>>>>> 7201 -   Add materialized views
>>>>>>
>>>>>> tripal_project module :
>>>>>> 7200 -   This is the required update for tripal_project when upgrading from Drupal core API 6.x.
>>>>>>
>>>>>> tripal_analysis module :
>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>
>>>>>> tripal_featuremap module :
>>>>>> 7200 -   This is the required update for tripal_featuremap when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>> 7202 -   Fixes a typo when setting the default CV for the unittype_id field of the featuremap table.
>>>>>>
>>>>>> tripal_feature module :
>>>>>> 7200 -   This is the required update for tripal_feature when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>> 7202 -   Adds the temporary tables used for loading GFF files.
>>>>>>
>>>>>> tripal_views module :
>>>>>> 7200 -   Tripal Views Update for 7.x-2.0    - Add relationship_only field to tripal_views_join    - Add relationship_handler field to tripal_views_join
>>>>>>
>>>>>> tripal_pub module :
>>>>>> 7202 -   Updates path of tripal_pub OBO to be relative.
>>>>>>
>>>>>> Performed update: tripal_feature_update_7200                                                    [ok]
>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>> does not exist
>>>>>> LINE 3: tripal_mviews tm
>>>>>>       ^
>>>>>> Performed update: tripal_feature_update_7201                                                    [ok]
>>>>>> Performed update: tripal_featuremap_update_7200                                                 [ok]
>>>>>> Performed update: tripal_featuremap_update_7201                                                 [ok]
>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>
>>>>>> Fatal error: Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>> Finished performing updates.                                                                    [ok]
>>>>>>
>>>>>>
>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------
>>>>>> Full output after setting search_path to public, chado
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>> _______________________________________________
>>>>>> Gmod-tripal mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>> ------------------------------------------------------------------------------
>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>> _______________________________________________
>>>>> Gmod-tripal mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>> _______________________________________________
>>> Gmod-tripal mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Stephen Ficklin-2
Hi Michael,

The fixes are ready.  I have also adjusted the upgrade documentation to
add a patch for a taxonomy bug that seems to occur for some people
during upgrade.  I added a new step #10 to the upgrade documentation
http://tripal.info/tutorials/v2.0/upgrade.    I also just released
Tripal v2.1-beta1.  This is a precursor for our full Tripal v2.1 release
(which will include support for Chado v1.3).

So, in step #14 when it asks you download Tripal use this command instead

drush pm-download tripal 7.x-2.1-beta1

Drupal only rebuilds its releases at the end of the day so this beta
release should be available tomorrow.

I have tested an upgrade of Drupal 6 / Tripal v1 to Drupal 7 / Tripal v2
and it worked just fine without problems using this new beta1 version.

Let me know if you have issues.

Stephen


On 1/22/2016 10:26 AM, Michael Dondrup wrote:

> Hi Stephen,
>
> That would be great, we will just revert to the state directly after updating clean drupal core
> next week.
> Will php 5.3.3 and drush 6.7.0 be ok?
>
> Michael
>
>
> On Jan 22, 2016, at 6:31 PM, Stephen Ficklin wrote:
>
>> Hi Michael,
>>
>> I believe I understand what the problem is.   I'm going to add a fix to Tripal v2.x (the development branch) and let you know when it's ready.  Can you use the development branch for testing your upgrade?  We're very close to releasing v2.1 so it should be stable enough to use.
>>
>> Stephen
>>
>> On 1/22/2016 2:39 AM, Michael Dondrup wrote:
>>> Hi,
>>> we are still getting the 'undefined function errors' for functions that are in reality defined in the code of tripal:
>>> e.g. tripal_add_mview() or tripal_insert_obo(). These functions sometimes change erratically throughout the process.
>>> We were suspecting the drush version as we were initially using drush 5.7, we have therefore tested with other
>>> versions: 6.4 (as recommended in the documentation), 6.0, 6.7 (latest stable 6), 5.5.9. We also tried drush 7 branches, but
>>> these don't recognize a drupal site.
>>>
>>> Drush install via composer, php version is PHP 5.3.3
>>>
>>> Each time we cleared the cache (drush cc all) and rebuilt the drush registry (drush rr). To no avail. As the process is a bit erratic
>>> I interpret this as caused by the sequence of php file inclusions.
>>>
>>> We have certainly hit a wall here, and would appreciate any input as the migration is somewhat urgent to cmplete.
>>>
>>> Thank you in advance for your help.
>>>
>>> Michael
>>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>> Full output below:
>>>
>>> $ drush updb
>>>   Tripal_core        7204  Adds the tripal_variable_terms and a tripal_node_variables tables
>>>   Tripal_feature     7202  Adds the temporary tables used for loading GFF files.
>>>   Tripal_pub         7202  Updates path of tripal_pub OBO to be relative.
>>>   Tripal_stock       7201  Add materialized views
>>>   Tripal_contact     7202  Updates path of tripal_contact OBO to be relative.
>>>   Tripal_featuremap  7202  Fixes a typo when setting the default CV for the unittype_id field of the
>>>                            featuremap table.
>>> Do you wish to run all pending updates? (y/n): y
>>> PHP Fatal error:  Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>
>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>> Error: Call to undefined function tripal_insert_obo() in
>>> /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install, line 409
>>> The external command could not be executed due to an application error.                         [error]
>>> 'all' cache was cleared in self                                                                 [success]
>>> Finished performing updates.                                                                    [ok]
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Jan 21, 2016, at 9:32 PM, Michael Dondrup wrote:
>>>
>>>> Hi Stephen,
>>>>
>>>> thank your for your response, I think we are getting closer to the core of the problem.
>>>> Do you think this might cause also the 'call to undefined function' error?
>>>>
>>>> Michael
>>>>
>>>> On Jan 21, 2016, at 8:00 PM, Stephen Ficklin wrote:
>>>>
>>>>> Hi Michael,
>>>>>
>>>>> When you started your upgrade did you have the search_path set for the postrgreSQL user?
>>>> Yes we had re-set the search path to public only.
>>>>
>>>>
>>>>> (Step 3 in upgrade procedue http://tripal.info/tutorials/v2.0/upgrade).  If so, then perhaps some of the tables that should be in the 'public' schema in your D6 site are in the 'chado' schema and they shouldn't be.
>>>> I think this is the case: The following tripal* tables are in chado in our D6 system:
>>>>
>>>> licebase=> \dt chado.tripal*
>>>>                 List of relations
>>>> Schema |         Name         | Type  |  Owner
>>>> --------+----------------------+-------+----------
>>>> chado  | tripal_custom_tables | table | lb_admin
>>>> chado  | tripal_gff_temp      | table | lb_admin
>>>> chado  | tripal_jobs          | table | lb_admin
>>>> chado  | tripal_mviews        | table | lb_admin
>>>> chado  | tripal_obo_temp      | table | lb_admin
>>>> (5 rows)
>>>>
>>>> The following ones are in public
>>>>
>>>> licebase=> \dt public.tripal*
>>>>                     List of relations
>>>> Schema |             Name             | Type  |  Owner
>>>> --------+------------------------------+-------+----------
>>>> public | tripal_analysis              | table | lb_admin
>>>> public | tripal_analysis_blast        | table | lb_admin
>>>> public | tripal_bulk_loader           | table | lb_admin
>>>> public | tripal_bulk_loader_constants | table | lb_admin
>>>> public | tripal_bulk_loader_inserted  | table | lb_admin
>>>> public | tripal_bulk_loader_template  | table | lb_admin
>>>> public | tripal_cv_obo                | table | lb_admin
>>>> public | tripal_feature_relagg        | table | lb_admin
>>>> public | tripal_pub_import            | table | lb_admin
>>>> public | tripal_views                 | table | lb_admin
>>>> public | tripal_views_field           | table | lb_admin
>>>> public | tripal_views_handlers        | table | lb_admin
>>>> public | tripal_views_join            | table | lb_admin
>>>> (13 rows)
>>>>
>>>>
>>>>
>>>>
>>>>>   I do remember a bug at one point in one of our development versions that caused this.  If this is the case then it makes sense that you would have problems during the upgrade.   Do you have a backup of your D6 site database where you can look to see if those tables are in the 'chado' schema?
>>>> W are working on an identical copy, while the D6 Tripal1 system is still online and we have backups of each stage so we can start over. So I could just look it up in the
>>>> production system.
>>>>
>>>>
>>>>> If so, moving them to the 'public' schema and then retrying the upgrade may help.  If you do see some of these tables in the 'chado' schema but you're unsure if there are more that should also be moved feel free to send the list of tables in your 'chado' schema and I can let you know.
>>>> So should I first attempt move all those tripal* tables from chado to public? Funny enough this doesn't cause problems in the D6 system....
>>>>
>>>>
>>>>> Stephen
>>>>>
>>>>> On 1/21/2016 1:15 AM, Michael Dondrup wrote:
>>>>>> Hi,
>>>>>> we fixed the first problem somehow the tripal_custom_tables table was created in chado schema. I moved it
>>>>>> ALTER TABLE tripal_custom_tables SET SCHEMA public;
>>>>>>
>>>>>> Leaving me with this error:
>>>>>>
>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>
>>>>>>
>>>>>> This is weird because the function is certainly defined in tripal/tripal_cv/api/tripal_cv.api.inc:function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE)
>>>>>>
>>>>>> I have tried to drush cc all and even rebuilt the registry as described here: https://www.drupal.org/project/registry_rebuild
>>>>>>
>>>>>> But to no avail. Anybody else having this problem?
>>>>>>
>>>>>> I really appreciate your help.
>>>>>>
>>>>>> Michael
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Jan 20, 2016, at 2:17 PM, Michael Dondrup wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> we are doing a test-run of the D6->7 migration of our site including a Tripal update, following http://tripal.info/tutorials/v2.0/upgrade
>>>>>>>
>>>>>>> We are currently at step 14. Next, apply the Tripal updates: drush updatedb
>>>>>>>
>>>>>>> All core updates, views and ctools have been performed without error and no pending db updates were scheduled prior to this step.
>>>>>>>
>>>>>>>
>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>> does not exist
>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>        ^
>>>>>>>
>>>>>>> [...]
>>>>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>
>>>>>>> I guess we have a fix for the first one, however that yields different errors:
>>>>>>>
>>>>>>> The table tripal_mviews exists but in the schema chado. I tried to set the search_path back:
>>>>>>> ALTER USER user SET search_path TO public, chado;
>>>>>>>
>>>>>>> However this yields other errors:
>>>>>>>
>>>>>>> Cannot add field tripal_custom_tables.mview_id: table doesn't exist.                            [error]
>>>>>>> [...]
>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install on line 449
>>>>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install, line 449
>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>
>>>>>>>
>>>>>>> I searched and found http://sourceforge.net/p/gmod/mailman/message/32762105/ but that doesn't seem to fit.
>>>>>>>
>>>>>>> Best
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Michael Dondrup
>>>>>>> Researcher
>>>>>>> Sea Lice Research Centre
>>>>>>> Department of Informatics
>>>>>>> University of Bergen
>>>>>>> Thormøhlensgate 55, N-5008 Bergen,
>>>>>>> Norway
>>>>>>>
>>>>>>>
>>>>>>> Full output of drush updatedb first iteration:
>>>>>>>
>>>>>>> $ drush updatedb
>>>>>>> The following updates are pending:
>>>>>>>
>>>>>>> tripal_core module :
>>>>>>> 7200 -   Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table
>>>>>>> 7201 -   Fixes missing language for nodes and URL aliases. This may take awhile...
>>>>>>> 7202 -   Adds a tripal_token_formats table for custom page titles and URL paths
>>>>>>> 7203 -   Adds a tripal_toc table for customizing the table of contents on each Tripal page.
>>>>>>> 7204 -   Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>>
>>>>>>> tripal_organism module :
>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>
>>>>>>> tripal_cv module :
>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>
>>>>>>> tripal_contact module :
>>>>>>> 7200 -   This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>> 7202 -   Updates path of tripal_contact OBO to be relative.
>>>>>>>
>>>>>>> tripal_bulk_loader module :
>>>>>>> 7200 -   Implements hook_update_N().   Update to 7.x-2.0  -Cast tripal_bulk_loader.template_id to int field
>>>>>>>
>>>>>>> tripal_library module :
>>>>>>> 7200 -   This is the required update for tripal_library when upgrading from Drupal core API 6.x.
>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>
>>>>>>> tripal_stock module :
>>>>>>> 7200 -   This is the required update for tripal_stock when upgrading from Drupal core API 6.x.
>>>>>>> 7201 -   Add materialized views
>>>>>>>
>>>>>>> tripal_project module :
>>>>>>> 7200 -   This is the required update for tripal_project when upgrading from Drupal core API 6.x.
>>>>>>>
>>>>>>> tripal_analysis module :
>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>
>>>>>>> tripal_featuremap module :
>>>>>>> 7200 -   This is the required update for tripal_featuremap when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>> 7202 -   Fixes a typo when setting the default CV for the unittype_id field of the featuremap table.
>>>>>>>
>>>>>>> tripal_feature module :
>>>>>>> 7200 -   This is the required update for tripal_feature when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>> 7202 -   Adds the temporary tables used for loading GFF files.
>>>>>>>
>>>>>>> tripal_views module :
>>>>>>> 7200 -   Tripal Views Update for 7.x-2.0    - Add relationship_only field to tripal_views_join    - Add relationship_handler field to tripal_views_join
>>>>>>>
>>>>>>> tripal_pub module :
>>>>>>> 7202 -   Updates path of tripal_pub OBO to be relative.
>>>>>>>
>>>>>>> Performed update: tripal_feature_update_7200                                                    [ok]
>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>> does not exist
>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>        ^
>>>>>>> Performed update: tripal_feature_update_7201                                                    [ok]
>>>>>>> Performed update: tripal_featuremap_update_7200                                                 [ok]
>>>>>>> Performed update: tripal_featuremap_update_7201                                                 [ok]
>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>
>>>>>>> Fatal error: Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>> Finished performing updates.                                                                    [ok]
>>>>>>>
>>>>>>>
>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>> Full output after setting search_path to public, chado
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>> _______________________________________________
>>>>>>> Gmod-tripal mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>> ------------------------------------------------------------------------------
>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>> _______________________________________________
>>>>>> Gmod-tripal mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>> ------------------------------------------------------------------------------
>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>> Monitor end-to-end web transactions and take corrective actions now
>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>> _______________________________________________
>>>> Gmod-tripal mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Stephen Ficklin-2
Hi Michael,

I found one irritating bug that should have been fixed for the beta1
release. I've fixed it but Drupal.org won't let me redo the release to
include the fix, so I had to issue a new beta2 release.  Also, I'm not
sure the command I gave you below to download Tripal will work, and I
can't test it to make sure until Drupal creates the files.  So use this
instead:

git clone [hidden email]:tripal/tripal.git -b 7.x-2.1-beta2

Stephen

On 1/23/2016 11:02 AM, Stephen Ficklin wrote:

> Hi Michael,
>
> The fixes are ready.  I have also adjusted the upgrade documentation
> to add a patch for a taxonomy bug that seems to occur for some people
> during upgrade.  I added a new step #10 to the upgrade documentation
> http://tripal.info/tutorials/v2.0/upgrade.    I also just released
> Tripal v2.1-beta1.  This is a precursor for our full Tripal v2.1
> release (which will include support for Chado v1.3).
>
> So, in step #14 when it asks you download Tripal use this command instead
>
> drush pm-download tripal 7.x-2.1-beta1
>
> Drupal only rebuilds its releases at the end of the day so this beta
> release should be available tomorrow.
>
> I have tested an upgrade of Drupal 6 / Tripal v1 to Drupal 7 / Tripal
> v2 and it worked just fine without problems using this new beta1 version.
>
> Let me know if you have issues.
>
> Stephen
>
>
> On 1/22/2016 10:26 AM, Michael Dondrup wrote:
>> Hi Stephen,
>>
>> That would be great, we will just revert to the state directly after
>> updating clean drupal core
>> next week.
>> Will php 5.3.3 and drush 6.7.0 be ok?
>>
>> Michael
>>
>>
>> On Jan 22, 2016, at 6:31 PM, Stephen Ficklin wrote:
>>
>>> Hi Michael,
>>>
>>> I believe I understand what the problem is.   I'm going to add a fix
>>> to Tripal v2.x (the development branch) and let you know when it's
>>> ready.  Can you use the development branch for testing your
>>> upgrade?  We're very close to releasing v2.1 so it should be stable
>>> enough to use.
>>>
>>> Stephen
>>>
>>> On 1/22/2016 2:39 AM, Michael Dondrup wrote:
>>>> Hi,
>>>> we are still getting the 'undefined function errors' for functions
>>>> that are in reality defined in the code of tripal:
>>>> e.g. tripal_add_mview() or tripal_insert_obo(). These functions
>>>> sometimes change erratically throughout the process.
>>>> We were suspecting the drush version as we were initially using
>>>> drush 5.7, we have therefore tested with other
>>>> versions: 6.4 (as recommended in the documentation), 6.0, 6.7
>>>> (latest stable 6), 5.5.9. We also tried drush 7 branches, but
>>>> these don't recognize a drupal site.
>>>>
>>>> Drush install via composer, php version is PHP 5.3.3
>>>>
>>>> Each time we cleared the cache (drush cc all) and rebuilt the drush
>>>> registry (drush rr). To no avail. As the process is a bit erratic
>>>> I interpret this as caused by the sequence of php file inclusions.
>>>>
>>>> We have certainly hit a wall here, and would appreciate any input
>>>> as the migration is somewhat urgent to cmplete.
>>>>
>>>> Thank you in advance for your help.
>>>>
>>>> Michael
>>>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>
>>>> Full output below:
>>>>
>>>> $ drush updb
>>>>   Tripal_core        7204  Adds the tripal_variable_terms and a
>>>> tripal_node_variables tables
>>>>   Tripal_feature     7202  Adds the temporary tables used for
>>>> loading GFF files.
>>>>   Tripal_pub         7202  Updates path of tripal_pub OBO to be
>>>> relative.
>>>>   Tripal_stock       7201  Add materialized views
>>>>   Tripal_contact     7202  Updates path of tripal_contact OBO to be
>>>> relative.
>>>>   Tripal_featuremap  7202  Fixes a typo when setting the default CV
>>>> for the unittype_id field of the
>>>>                            featuremap table.
>>>> Do you wish to run all pending updates? (y/n): y
>>>> PHP Fatal error:  Call to undefined function tripal_insert_obo() in
>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install
>>>> on line 409
>>>>
>>>> Fatal error: Call to undefined function tripal_insert_obo() in
>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install
>>>> on line 409
>>>> Drush command terminated abnormally due to an unrecoverable
>>>> error.                              [error]
>>>> Error: Call to undefined function tripal_insert_obo() in
>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install,
>>>> line 409
>>>> The external command could not be executed due to an application
>>>> error.                         [error]
>>>> 'all' cache was cleared in self [success]
>>>> Finished performing updates. [ok]
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Jan 21, 2016, at 9:32 PM, Michael Dondrup wrote:
>>>>
>>>>> Hi Stephen,
>>>>>
>>>>> thank your for your response, I think we are getting closer to the
>>>>> core of the problem.
>>>>> Do you think this might cause also the 'call to undefined
>>>>> function' error?
>>>>>
>>>>> Michael
>>>>>
>>>>> On Jan 21, 2016, at 8:00 PM, Stephen Ficklin wrote:
>>>>>
>>>>>> Hi Michael,
>>>>>>
>>>>>> When you started your upgrade did you have the search_path set
>>>>>> for the postrgreSQL user?
>>>>> Yes we had re-set the search path to public only.
>>>>>
>>>>>
>>>>>> (Step 3 in upgrade procedue
>>>>>> http://tripal.info/tutorials/v2.0/upgrade).  If so, then perhaps
>>>>>> some of the tables that should be in the 'public' schema in your
>>>>>> D6 site are in the 'chado' schema and they shouldn't be.
>>>>> I think this is the case: The following tripal* tables are in
>>>>> chado in our D6 system:
>>>>>
>>>>> licebase=> \dt chado.tripal*
>>>>>                 List of relations
>>>>> Schema |         Name         | Type  |  Owner
>>>>> --------+----------------------+-------+----------
>>>>> chado  | tripal_custom_tables | table | lb_admin
>>>>> chado  | tripal_gff_temp      | table | lb_admin
>>>>> chado  | tripal_jobs          | table | lb_admin
>>>>> chado  | tripal_mviews        | table | lb_admin
>>>>> chado  | tripal_obo_temp      | table | lb_admin
>>>>> (5 rows)
>>>>>
>>>>> The following ones are in public
>>>>>
>>>>> licebase=> \dt public.tripal*
>>>>>                     List of relations
>>>>> Schema |             Name             | Type  |  Owner
>>>>> --------+------------------------------+-------+----------
>>>>> public | tripal_analysis              | table | lb_admin
>>>>> public | tripal_analysis_blast        | table | lb_admin
>>>>> public | tripal_bulk_loader           | table | lb_admin
>>>>> public | tripal_bulk_loader_constants | table | lb_admin
>>>>> public | tripal_bulk_loader_inserted  | table | lb_admin
>>>>> public | tripal_bulk_loader_template  | table | lb_admin
>>>>> public | tripal_cv_obo                | table | lb_admin
>>>>> public | tripal_feature_relagg        | table | lb_admin
>>>>> public | tripal_pub_import            | table | lb_admin
>>>>> public | tripal_views                 | table | lb_admin
>>>>> public | tripal_views_field           | table | lb_admin
>>>>> public | tripal_views_handlers        | table | lb_admin
>>>>> public | tripal_views_join            | table | lb_admin
>>>>> (13 rows)
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>   I do remember a bug at one point in one of our development
>>>>>> versions that caused this.  If this is the case then it makes
>>>>>> sense that you would have problems during the upgrade.   Do you
>>>>>> have a backup of your D6 site database where you can look to see
>>>>>> if those tables are in the 'chado' schema?
>>>>> W are working on an identical copy, while the D6 Tripal1 system is
>>>>> still online and we have backups of each stage so we can start
>>>>> over. So I could just look it up in the
>>>>> production system.
>>>>>
>>>>>
>>>>>> If so, moving them to the 'public' schema and then retrying the
>>>>>> upgrade may help.  If you do see some of these tables in the
>>>>>> 'chado' schema but you're unsure if there are more that should
>>>>>> also be moved feel free to send the list of tables in your
>>>>>> 'chado' schema and I can let you know.
>>>>> So should I first attempt move all those tripal* tables from chado
>>>>> to public? Funny enough this doesn't cause problems in the D6
>>>>> system....
>>>>>
>>>>>
>>>>>> Stephen
>>>>>>
>>>>>> On 1/21/2016 1:15 AM, Michael Dondrup wrote:
>>>>>>> Hi,
>>>>>>> we fixed the first problem somehow the tripal_custom_tables
>>>>>>> table was created in chado schema. I moved it
>>>>>>> ALTER TABLE tripal_custom_tables SET SCHEMA public;
>>>>>>>
>>>>>>> Leaving me with this error:
>>>>>>>
>>>>>>> PHP Fatal error:  Call to undefined function
>>>>>>> tripal_set_default_cv() in
>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install
>>>>>>> on line 655
>>>>>>>
>>>>>>>
>>>>>>> This is weird because the function is certainly defined in
>>>>>>> tripal/tripal_cv/api/tripal_cv.api.inc:function
>>>>>>> tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE)
>>>>>>>
>>>>>>> I have tried to drush cc all and even rebuilt the registry as
>>>>>>> described here: https://www.drupal.org/project/registry_rebuild
>>>>>>>
>>>>>>> But to no avail. Anybody else having this problem?
>>>>>>>
>>>>>>> I really appreciate your help.
>>>>>>>
>>>>>>> Michael
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Jan 20, 2016, at 2:17 PM, Michael Dondrup wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> we are doing a test-run of the D6->7 migration of our site
>>>>>>>> including a Tripal update, following
>>>>>>>> http://tripal.info/tutorials/v2.0/upgrade
>>>>>>>>
>>>>>>>> We are currently at step 14. Next, apply the Tripal updates:
>>>>>>>> drush updatedb
>>>>>>>>
>>>>>>>> All core updates, views and ctools have been performed without
>>>>>>>> error and no pending db updates were scheduled prior to this step.
>>>>>>>>
>>>>>>>>
>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7
>>>>>>>> ERROR:  relation "tripal_mviews"   [error]
>>>>>>>> does not exist
>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>        ^
>>>>>>>>
>>>>>>>> [...]
>>>>>>>> Drush command terminated abnormally due to an unrecoverable
>>>>>>>> error. [error]
>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install,
>>>>>>>> line 655
>>>>>>>> The external command could not be executed due to an
>>>>>>>> application error.                         [error]
>>>>>>>>
>>>>>>>> I guess we have a fix for the first one, however that yields
>>>>>>>> different errors:
>>>>>>>>
>>>>>>>> The table tripal_mviews exists but in the schema chado. I tried
>>>>>>>> to set the search_path back:
>>>>>>>> ALTER USER user SET search_path TO public, chado;
>>>>>>>>
>>>>>>>> However this yields other errors:
>>>>>>>>
>>>>>>>> Cannot add field tripal_custom_tables.mview_id: table doesn't
>>>>>>>> exist. [error]
>>>>>>>> [...]
>>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in
>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install
>>>>>>>> on line 449
>>>>>>>> Drush command terminated abnormally due to an unrecoverable
>>>>>>>> error. [error]
>>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install,
>>>>>>>> line 449
>>>>>>>> The external command could not be executed due to an
>>>>>>>> application error.                         [error]
>>>>>>>>
>>>>>>>>
>>>>>>>> I searched and found
>>>>>>>> http://sourceforge.net/p/gmod/mailman/message/32762105/ but
>>>>>>>> that doesn't seem to fit.
>>>>>>>>
>>>>>>>> Best
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Michael Dondrup
>>>>>>>> Researcher
>>>>>>>> Sea Lice Research Centre
>>>>>>>> Department of Informatics
>>>>>>>> University of Bergen
>>>>>>>> Thormøhlensgate 55, N-5008 Bergen,
>>>>>>>> Norway
>>>>>>>>
>>>>>>>>
>>>>>>>> Full output of drush updatedb first iteration:
>>>>>>>>
>>>>>>>> $ drush updatedb
>>>>>>>> The following updates are pending:
>>>>>>>>
>>>>>>>> tripal_core module :
>>>>>>>> 7200 -   Adds an mview_id column to the tripal_custom_tables
>>>>>>>> table and makes an assocation between the mview and the custom
>>>>>>>> table
>>>>>>>> 7201 -   Fixes missing language for nodes and URL aliases. This
>>>>>>>> may take awhile...
>>>>>>>> 7202 -   Adds a tripal_token_formats table for custom page
>>>>>>>> titles and URL paths
>>>>>>>> 7203 -   Adds a tripal_toc table for customizing the table of
>>>>>>>> contents on each Tripal page.
>>>>>>>> 7204 -   Adds the tripal_variable_terms and a
>>>>>>>> tripal_node_variables tables
>>>>>>>>
>>>>>>>> tripal_organism module :
>>>>>>>> 7200 -   This is the required update for tripal_organism when
>>>>>>>> upgrading from Drupal core API 6.x.
>>>>>>>>
>>>>>>>> tripal_cv module :
>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>
>>>>>>>> tripal_contact module :
>>>>>>>> 7200 -   This is the required update for tripal_contact when
>>>>>>>> upgrading from Drupal core API 6.x.
>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>> 7202 -   Updates path of tripal_contact OBO to be relative.
>>>>>>>>
>>>>>>>> tripal_bulk_loader module :
>>>>>>>> 7200 -   Implements hook_update_N().   Update to 7.x-2.0  -Cast
>>>>>>>> tripal_bulk_loader.template_id to int field
>>>>>>>>
>>>>>>>> tripal_library module :
>>>>>>>> 7200 -   This is the required update for tripal_library when
>>>>>>>> upgrading from Drupal core API 6.x.
>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>
>>>>>>>> tripal_stock module :
>>>>>>>> 7200 -   This is the required update for tripal_stock when
>>>>>>>> upgrading from Drupal core API 6.x.
>>>>>>>> 7201 -   Add materialized views
>>>>>>>>
>>>>>>>> tripal_project module :
>>>>>>>> 7200 -   This is the required update for tripal_project when
>>>>>>>> upgrading from Drupal core API 6.x.
>>>>>>>>
>>>>>>>> tripal_analysis module :
>>>>>>>> 7200 -   This is the required update for tripal_organism when
>>>>>>>> upgrading from Drupal core API 6.x.
>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>
>>>>>>>> tripal_featuremap module :
>>>>>>>> 7200 -   This is the required update for tripal_featuremap when
>>>>>>>> upgrading from Drupal core API 6.x.  This update may take some
>>>>>>>> time to complete.
>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>> 7202 -   Fixes a typo when setting the default CV for the
>>>>>>>> unittype_id field of the featuremap table.
>>>>>>>>
>>>>>>>> tripal_feature module :
>>>>>>>> 7200 -   This is the required update for tripal_feature when
>>>>>>>> upgrading from Drupal core API 6.x.  This update may take some
>>>>>>>> time to complete.
>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>> 7202 -   Adds the temporary tables used for loading GFF files.
>>>>>>>>
>>>>>>>> tripal_views module :
>>>>>>>> 7200 -   Tripal Views Update for 7.x-2.0    - Add
>>>>>>>> relationship_only field to tripal_views_join    - Add
>>>>>>>> relationship_handler field to tripal_views_join
>>>>>>>>
>>>>>>>> tripal_pub module :
>>>>>>>> 7202 -   Updates path of tripal_pub OBO to be relative.
>>>>>>>>
>>>>>>>> Performed update: tripal_feature_update_7200 [ok]
>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7
>>>>>>>> ERROR:  relation "tripal_mviews"   [error]
>>>>>>>> does not exist
>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>        ^
>>>>>>>> Performed update: tripal_feature_update_7201 [ok]
>>>>>>>> Performed update: tripal_featuremap_update_7200 [ok]
>>>>>>>> Performed update: tripal_featuremap_update_7201 [ok]
>>>>>>>> PHP Fatal error:  Call to undefined function
>>>>>>>> tripal_set_default_cv() in
>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install
>>>>>>>> on line 655
>>>>>>>>
>>>>>>>> Fatal error: Call to undefined function tripal_set_default_cv()
>>>>>>>> in
>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install
>>>>>>>> on line 655
>>>>>>>> Drush command terminated abnormally due to an unrecoverable
>>>>>>>> error. [error]
>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install,
>>>>>>>> line 655
>>>>>>>> The external command could not be executed due to an
>>>>>>>> application error.                         [error]
>>>>>>>> Finished performing updates. [ok]
>>>>>>>>
>>>>>>>>
>>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>
>>>>>>>> Full output after setting search_path to public, chado
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>
>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application
>>>>>>>> Performance
>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>> Monitor end-to-end web transactions and take corrective actions
>>>>>>>> now
>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-tripal mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>> ------------------------------------------------------------------------------
>>>>>>>
>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application
>>>>>>> Performance
>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>> _______________________________________________
>>>>>>> Gmod-tripal mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>> ------------------------------------------------------------------------------
>>>>>
>>>>> Site24x7 APM Insight: Get Deep Visibility into Application
>>>>> Performance
>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>> _______________________________________________
>>>>> Gmod-tripal mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Michael Dondrup-3
Hi,

thank you again. It worked!

The dbupdate has been applied using the updated code.  There was only one repeated warning.

in updating tripal_views
 [site https://...] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store relationship for studyprop_feature => feature when you should be using tripal_views_joins.

I think we should take another snapshot here and start activating tripal core modules and see how that goes.

Best
Michael


----------------------------------------------------------------------------------------------------------------------------------------------
Below I will list the commands for our reference:

# ALTER USER user SET search_path TO public; just to be shure

## applied taxonomy patch, but didn't start core update from scratch becasue we didn't have taxonomy errors

### starting from Snapshot step_12

## moved misplaced tables from chado to public in psql

ALTER table chado.tripal_custom_tables set schema public;
ALTER table chado.tripal_gff_temp set schema public;
ALTER table chado.tripal_jobs set schema public;
ALTER table chado.tripal_mviews set schema public;
ALTER table chado.tripal_obo_temp set schema public;


### Step 13.
drush pm-download views ctools
drush updatedb

drush pm-enable ctools views views_ui

## all OK Snapshot taken step_13

### Step 14. modified to get latest beta

cd sites/all/modules
git clone https://github.com/tripal/tripal.git -b 7.x-2.1-beta2
# warning: Remote branch 7.x-2.1-beta2 not found in upstream origin, using HEAD instead
cd tripal/
## 7.x-2.1-beta2 is a tag
git checkout 7.x-2.1-beta2

### Step 15:
drush updatedb
## all ok

### Step 16:

drush pm-enable tripal_core
## all ok
drush pm-enable tripal_views

# repeated many times
# [site https://...] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store
# relationship for studyprop_feature => feature when you should be using tripal_views_joins.

### Step 17: Administration -> Tripal -> Views Integration -> click 'Delete All Integrations'
# Successfully deleted all views integration.
#Successfully rebuilt default Tripal Views Integrations

## Changed tripal_core.info to avoid update warnings
> version = 7.x-2.1-beta2



On Jan 24, 2016, at 11:17 AM, Michael Dondrup wrote:

> Hi Stephen,
> thank you so much for the quick response. I need to get our sysadmin involved to revert the database
> to the correct snapshot. I hope I will be ready testing before the afternoon on monday.
>
> Michael
>
> On Jan 23, 2016, at 9:11 PM, Stephen Ficklin wrote:
>
>> Hi Michael,
>>
>> I found one irritating bug that should have been fixed for the beta1 release. I've fixed it but Drupal.org won't let me redo the release to include the fix, so I had to issue a new beta2 release.  Also, I'm not sure the command I gave you below to download Tripal will work, and I can't test it to make sure until Drupal creates the files.  So use this instead:
>>
>> git clone [hidden email]:tripal/tripal.git -b 7.x-2.1-beta2
>>
>> Stephen
>>
>> On 1/23/2016 11:02 AM, Stephen Ficklin wrote:
>>> Hi Michael,
>>>
>>> The fixes are ready.  I have also adjusted the upgrade documentation to add a patch for a taxonomy bug that seems to occur for some people during upgrade.  I added a new step #10 to the upgrade documentation http://tripal.info/tutorials/v2.0/upgrade.    I also just released Tripal v2.1-beta1.  This is a precursor for our full Tripal v2.1 release (which will include support for Chado v1.3).
>>>
>>> So, in step #14 when it asks you download Tripal use this command instead
>>>
>>> drush pm-download tripal 7.x-2.1-beta1
>>>
>>> Drupal only rebuilds its releases at the end of the day so this beta release should be available tomorrow.
>>>
>>> I have tested an upgrade of Drupal 6 / Tripal v1 to Drupal 7 / Tripal v2 and it worked just fine without problems using this new beta1 version.
>>>
>>> Let me know if you have issues.
>>>
>>> Stephen
>>>
>>>
>>> On 1/22/2016 10:26 AM, Michael Dondrup wrote:
>>>> Hi Stephen,
>>>>
>>>> That would be great, we will just revert to the state directly after updating clean drupal core
>>>> next week.
>>>> Will php 5.3.3 and drush 6.7.0 be ok?
>>>>
>>>> Michael
>>>>
>>>>
>>>> On Jan 22, 2016, at 6:31 PM, Stephen Ficklin wrote:
>>>>
>>>>> Hi Michael,
>>>>>
>>>>> I believe I understand what the problem is.   I'm going to add a fix to Tripal v2.x (the development branch) and let you know when it's ready.  Can you use the development branch for testing your upgrade?  We're very close to releasing v2.1 so it should be stable enough to use.
>>>>>
>>>>> Stephen
>>>>>
>>>>> On 1/22/2016 2:39 AM, Michael Dondrup wrote:
>>>>>> Hi,
>>>>>> we are still getting the 'undefined function errors' for functions that are in reality defined in the code of tripal:
>>>>>> e.g. tripal_add_mview() or tripal_insert_obo(). These functions sometimes change erratically throughout the process.
>>>>>> We were suspecting the drush version as we were initially using drush 5.7, we have therefore tested with other
>>>>>> versions: 6.4 (as recommended in the documentation), 6.0, 6.7 (latest stable 6), 5.5.9. We also tried drush 7 branches, but
>>>>>> these don't recognize a drupal site.
>>>>>>
>>>>>> Drush install via composer, php version is PHP 5.3.3
>>>>>>
>>>>>> Each time we cleared the cache (drush cc all) and rebuilt the drush registry (drush rr). To no avail. As the process is a bit erratic
>>>>>> I interpret this as caused by the sequence of php file inclusions.
>>>>>>
>>>>>> We have certainly hit a wall here, and would appreciate any input as the migration is somewhat urgent to cmplete.
>>>>>>
>>>>>> Thank you in advance for your help.
>>>>>>
>>>>>> Michael
>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>> Full output below:
>>>>>>
>>>>>> $ drush updb
>>>>>> Tripal_core        7204  Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>> Tripal_feature     7202  Adds the temporary tables used for loading GFF files.
>>>>>> Tripal_pub         7202  Updates path of tripal_pub OBO to be relative.
>>>>>> Tripal_stock       7201  Add materialized views
>>>>>> Tripal_contact     7202  Updates path of tripal_contact OBO to be relative.
>>>>>> Tripal_featuremap  7202  Fixes a typo when setting the default CV for the unittype_id field of the
>>>>>>                          featuremap table.
>>>>>> Do you wish to run all pending updates? (y/n): y
>>>>>> PHP Fatal error:  Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>>>>
>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install, line 409
>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>> 'all' cache was cleared in self [success]
>>>>>> Finished performing updates. [ok]
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Jan 21, 2016, at 9:32 PM, Michael Dondrup wrote:
>>>>>>
>>>>>>> Hi Stephen,
>>>>>>>
>>>>>>> thank your for your response, I think we are getting closer to the core of the problem.
>>>>>>> Do you think this might cause also the 'call to undefined function' error?
>>>>>>>
>>>>>>> Michael
>>>>>>>
>>>>>>> On Jan 21, 2016, at 8:00 PM, Stephen Ficklin wrote:
>>>>>>>
>>>>>>>> Hi Michael,
>>>>>>>>
>>>>>>>> When you started your upgrade did you have the search_path set for the postrgreSQL user?
>>>>>>> Yes we had re-set the search path to public only.
>>>>>>>
>>>>>>>
>>>>>>>> (Step 3 in upgrade procedue http://tripal.info/tutorials/v2.0/upgrade).  If so, then perhaps some of the tables that should be in the 'public' schema in your D6 site are in the 'chado' schema and they shouldn't be.
>>>>>>> I think this is the case: The following tripal* tables are in chado in our D6 system:
>>>>>>>
>>>>>>> licebase=> \dt chado.tripal*
>>>>>>>               List of relations
>>>>>>> Schema |         Name         | Type  |  Owner
>>>>>>> --------+----------------------+-------+----------
>>>>>>> chado  | tripal_custom_tables | table | lb_admin
>>>>>>> chado  | tripal_gff_temp      | table | lb_admin
>>>>>>> chado  | tripal_jobs          | table | lb_admin
>>>>>>> chado  | tripal_mviews        | table | lb_admin
>>>>>>> chado  | tripal_obo_temp      | table | lb_admin
>>>>>>> (5 rows)
>>>>>>>
>>>>>>> The following ones are in public
>>>>>>>
>>>>>>> licebase=> \dt public.tripal*
>>>>>>>                   List of relations
>>>>>>> Schema |             Name             | Type  |  Owner
>>>>>>> --------+------------------------------+-------+----------
>>>>>>> public | tripal_analysis              | table | lb_admin
>>>>>>> public | tripal_analysis_blast        | table | lb_admin
>>>>>>> public | tripal_bulk_loader           | table | lb_admin
>>>>>>> public | tripal_bulk_loader_constants | table | lb_admin
>>>>>>> public | tripal_bulk_loader_inserted  | table | lb_admin
>>>>>>> public | tripal_bulk_loader_template  | table | lb_admin
>>>>>>> public | tripal_cv_obo                | table | lb_admin
>>>>>>> public | tripal_feature_relagg        | table | lb_admin
>>>>>>> public | tripal_pub_import            | table | lb_admin
>>>>>>> public | tripal_views                 | table | lb_admin
>>>>>>> public | tripal_views_field           | table | lb_admin
>>>>>>> public | tripal_views_handlers        | table | lb_admin
>>>>>>> public | tripal_views_join            | table | lb_admin
>>>>>>> (13 rows)
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> I do remember a bug at one point in one of our development versions that caused this.  If this is the case then it makes sense that you would have problems during the upgrade.   Do you have a backup of your D6 site database where you can look to see if those tables are in the 'chado' schema?
>>>>>>> W are working on an identical copy, while the D6 Tripal1 system is still online and we have backups of each stage so we can start over. So I could just look it up in the
>>>>>>> production system.
>>>>>>>
>>>>>>>
>>>>>>>> If so, moving them to the 'public' schema and then retrying the upgrade may help.  If you do see some of these tables in the 'chado' schema but you're unsure if there are more that should also be moved feel free to send the list of tables in your 'chado' schema and I can let you know.
>>>>>>> So should I first attempt move all those tripal* tables from chado to public? Funny enough this doesn't cause problems in the D6 system....
>>>>>>>
>>>>>>>
>>>>>>>> Stephen
>>>>>>>>
>>>>>>>> On 1/21/2016 1:15 AM, Michael Dondrup wrote:
>>>>>>>>> Hi,
>>>>>>>>> we fixed the first problem somehow the tripal_custom_tables table was created in chado schema. I moved it
>>>>>>>>> ALTER TABLE tripal_custom_tables SET SCHEMA public;
>>>>>>>>>
>>>>>>>>> Leaving me with this error:
>>>>>>>>>
>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> This is weird because the function is certainly defined in tripal/tripal_cv/api/tripal_cv.api.inc:function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE)
>>>>>>>>>
>>>>>>>>> I have tried to drush cc all and even rebuilt the registry as described here: https://www.drupal.org/project/registry_rebuild
>>>>>>>>>
>>>>>>>>> But to no avail. Anybody else having this problem?
>>>>>>>>>
>>>>>>>>> I really appreciate your help.
>>>>>>>>>
>>>>>>>>> Michael
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Jan 20, 2016, at 2:17 PM, Michael Dondrup wrote:
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> we are doing a test-run of the D6->7 migration of our site including a Tripal update, following http://tripal.info/tutorials/v2.0/upgrade
>>>>>>>>>>
>>>>>>>>>> We are currently at step 14. Next, apply the Tripal updates: drush updatedb
>>>>>>>>>>
>>>>>>>>>> All core updates, views and ctools have been performed without error and no pending db updates were scheduled prior to this step.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>>>>> does not exist
>>>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>>>      ^
>>>>>>>>>>
>>>>>>>>>> [...]
>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>
>>>>>>>>>> I guess we have a fix for the first one, however that yields different errors:
>>>>>>>>>>
>>>>>>>>>> The table tripal_mviews exists but in the schema chado. I tried to set the search_path back:
>>>>>>>>>> ALTER USER user SET search_path TO public, chado;
>>>>>>>>>>
>>>>>>>>>> However this yields other errors:
>>>>>>>>>>
>>>>>>>>>> Cannot add field tripal_custom_tables.mview_id: table doesn't exist. [error]
>>>>>>>>>> [...]
>>>>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install on line 449
>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install, line 449
>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> I searched and found http://sourceforge.net/p/gmod/mailman/message/32762105/ but that doesn't seem to fit.
>>>>>>>>>>
>>>>>>>>>> Best
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Michael Dondrup
>>>>>>>>>> Researcher
>>>>>>>>>> Sea Lice Research Centre
>>>>>>>>>> Department of Informatics
>>>>>>>>>> University of Bergen
>>>>>>>>>> Thormøhlensgate 55, N-5008 Bergen,
>>>>>>>>>> Norway
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Full output of drush updatedb first iteration:
>>>>>>>>>>
>>>>>>>>>> $ drush updatedb
>>>>>>>>>> The following updates are pending:
>>>>>>>>>>
>>>>>>>>>> tripal_core module :
>>>>>>>>>> 7200 -   Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table
>>>>>>>>>> 7201 -   Fixes missing language for nodes and URL aliases. This may take awhile...
>>>>>>>>>> 7202 -   Adds a tripal_token_formats table for custom page titles and URL paths
>>>>>>>>>> 7203 -   Adds a tripal_toc table for customizing the table of contents on each Tripal page.
>>>>>>>>>> 7204 -   Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>>>>>
>>>>>>>>>> tripal_organism module :
>>>>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>>>>
>>>>>>>>>> tripal_cv module :
>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>
>>>>>>>>>> tripal_contact module :
>>>>>>>>>> 7200 -   This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
>>>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>>>> 7202 -   Updates path of tripal_contact OBO to be relative.
>>>>>>>>>>
>>>>>>>>>> tripal_bulk_loader module :
>>>>>>>>>> 7200 -   Implements hook_update_N().   Update to 7.x-2.0  -Cast tripal_bulk_loader.template_id to int field
>>>>>>>>>>
>>>>>>>>>> tripal_library module :
>>>>>>>>>> 7200 -   This is the required update for tripal_library when upgrading from Drupal core API 6.x.
>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>
>>>>>>>>>> tripal_stock module :
>>>>>>>>>> 7200 -   This is the required update for tripal_stock when upgrading from Drupal core API 6.x.
>>>>>>>>>> 7201 -   Add materialized views
>>>>>>>>>>
>>>>>>>>>> tripal_project module :
>>>>>>>>>> 7200 -   This is the required update for tripal_project when upgrading from Drupal core API 6.x.
>>>>>>>>>>
>>>>>>>>>> tripal_analysis module :
>>>>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>
>>>>>>>>>> tripal_featuremap module :
>>>>>>>>>> 7200 -   This is the required update for tripal_featuremap when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>>>> 7202 -   Fixes a typo when setting the default CV for the unittype_id field of the featuremap table.
>>>>>>>>>>
>>>>>>>>>> tripal_feature module :
>>>>>>>>>> 7200 -   This is the required update for tripal_feature when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>> 7202 -   Adds the temporary tables used for loading GFF files.
>>>>>>>>>>
>>>>>>>>>> tripal_views module :
>>>>>>>>>> 7200 -   Tripal Views Update for 7.x-2.0    - Add relationship_only field to tripal_views_join    - Add relationship_handler field to tripal_views_join
>>>>>>>>>>
>>>>>>>>>> tripal_pub module :
>>>>>>>>>> 7202 -   Updates path of tripal_pub OBO to be relative.
>>>>>>>>>>
>>>>>>>>>> Performed update: tripal_feature_update_7200 [ok]
>>>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>>>>> does not exist
>>>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>>>      ^
>>>>>>>>>> Performed update: tripal_feature_update_7201 [ok]
>>>>>>>>>> Performed update: tripal_featuremap_update_7200 [ok]
>>>>>>>>>> Performed update: tripal_featuremap_update_7201 [ok]
>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>
>>>>>>>>>> Fatal error: Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>> Finished performing updates. [ok]
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>>> Full output after setting search_path to public, chado
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>> [hidden email]
>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>> _______________________________________________
>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>> [hidden email]
>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>> _______________________________________________
>>>>>>> Gmod-tripal mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>
>>
>


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Stephen Ficklin-2
Wonderful!  Yes, those warnings will unfortunately appear.  But, after
you delete the view integrations (Step 17) they should be rebuilt and
that message should go away.  I have made note of these warnings in the
the upgrade instructions.

Thanks for reaching out when you had issues.

Stephen

On 1/25/2016 6:20 AM, Michael Dondrup wrote:

> Hi,
>
> thank you again. It worked!
>
> The dbupdate has been applied using the updated code.  There was only one repeated warning.
>
> in updating tripal_views
>   [site https://...] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store relationship for studyprop_feature => feature when you should be using tripal_views_joins.
>
> I think we should take another snapshot here and start activating tripal core modules and see how that goes.
>
> Best
> Michael
>
>
> ----------------------------------------------------------------------------------------------------------------------------------------------
> Below I will list the commands for our reference:
>
> # ALTER USER user SET search_path TO public; just to be shure
>
> ## applied taxonomy patch, but didn't start core update from scratch becasue we didn't have taxonomy errors
>
> ### starting from Snapshot step_12
>
> ## moved misplaced tables from chado to public in psql
>
> ALTER table chado.tripal_custom_tables set schema public;
> ALTER table chado.tripal_gff_temp set schema public;
> ALTER table chado.tripal_jobs set schema public;
> ALTER table chado.tripal_mviews set schema public;
> ALTER table chado.tripal_obo_temp set schema public;
>
>
> ### Step 13.
> drush pm-download views ctools
> drush updatedb
>
> drush pm-enable ctools views views_ui
>
> ## all OK Snapshot taken step_13
>
> ### Step 14. modified to get latest beta
>
> cd sites/all/modules
> git clone https://github.com/tripal/tripal.git -b 7.x-2.1-beta2
> # warning: Remote branch 7.x-2.1-beta2 not found in upstream origin, using HEAD instead
> cd tripal/
> ## 7.x-2.1-beta2 is a tag
> git checkout 7.x-2.1-beta2
>
> ### Step 15:
> drush updatedb
> ## all ok
>
> ### Step 16:
>
> drush pm-enable tripal_core
> ## all ok
> drush pm-enable tripal_views
>
> # repeated many times
> # [site https://...] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store
> # relationship for studyprop_feature => feature when you should be using tripal_views_joins.
>
> ### Step 17: Administration -> Tripal -> Views Integration -> click 'Delete All Integrations'
> # Successfully deleted all views integration.
> #Successfully rebuilt default Tripal Views Integrations
>
> ## Changed tripal_core.info to avoid update warnings
>> version = 7.x-2.1-beta2
>
>
> On Jan 24, 2016, at 11:17 AM, Michael Dondrup wrote:
>
>> Hi Stephen,
>> thank you so much for the quick response. I need to get our sysadmin involved to revert the database
>> to the correct snapshot. I hope I will be ready testing before the afternoon on monday.
>>
>> Michael
>>
>> On Jan 23, 2016, at 9:11 PM, Stephen Ficklin wrote:
>>
>>> Hi Michael,
>>>
>>> I found one irritating bug that should have been fixed for the beta1 release. I've fixed it but Drupal.org won't let me redo the release to include the fix, so I had to issue a new beta2 release.  Also, I'm not sure the command I gave you below to download Tripal will work, and I can't test it to make sure until Drupal creates the files.  So use this instead:
>>>
>>> git clone [hidden email]:tripal/tripal.git -b 7.x-2.1-beta2
>>>
>>> Stephen
>>>
>>> On 1/23/2016 11:02 AM, Stephen Ficklin wrote:
>>>> Hi Michael,
>>>>
>>>> The fixes are ready.  I have also adjusted the upgrade documentation to add a patch for a taxonomy bug that seems to occur for some people during upgrade.  I added a new step #10 to the upgrade documentation http://tripal.info/tutorials/v2.0/upgrade.    I also just released Tripal v2.1-beta1.  This is a precursor for our full Tripal v2.1 release (which will include support for Chado v1.3).
>>>>
>>>> So, in step #14 when it asks you download Tripal use this command instead
>>>>
>>>> drush pm-download tripal 7.x-2.1-beta1
>>>>
>>>> Drupal only rebuilds its releases at the end of the day so this beta release should be available tomorrow.
>>>>
>>>> I have tested an upgrade of Drupal 6 / Tripal v1 to Drupal 7 / Tripal v2 and it worked just fine without problems using this new beta1 version.
>>>>
>>>> Let me know if you have issues.
>>>>
>>>> Stephen
>>>>
>>>>
>>>> On 1/22/2016 10:26 AM, Michael Dondrup wrote:
>>>>> Hi Stephen,
>>>>>
>>>>> That would be great, we will just revert to the state directly after updating clean drupal core
>>>>> next week.
>>>>> Will php 5.3.3 and drush 6.7.0 be ok?
>>>>>
>>>>> Michael
>>>>>
>>>>>
>>>>> On Jan 22, 2016, at 6:31 PM, Stephen Ficklin wrote:
>>>>>
>>>>>> Hi Michael,
>>>>>>
>>>>>> I believe I understand what the problem is.   I'm going to add a fix to Tripal v2.x (the development branch) and let you know when it's ready.  Can you use the development branch for testing your upgrade?  We're very close to releasing v2.1 so it should be stable enough to use.
>>>>>>
>>>>>> Stephen
>>>>>>
>>>>>> On 1/22/2016 2:39 AM, Michael Dondrup wrote:
>>>>>>> Hi,
>>>>>>> we are still getting the 'undefined function errors' for functions that are in reality defined in the code of tripal:
>>>>>>> e.g. tripal_add_mview() or tripal_insert_obo(). These functions sometimes change erratically throughout the process.
>>>>>>> We were suspecting the drush version as we were initially using drush 5.7, we have therefore tested with other
>>>>>>> versions: 6.4 (as recommended in the documentation), 6.0, 6.7 (latest stable 6), 5.5.9. We also tried drush 7 branches, but
>>>>>>> these don't recognize a drupal site.
>>>>>>>
>>>>>>> Drush install via composer, php version is PHP 5.3.3
>>>>>>>
>>>>>>> Each time we cleared the cache (drush cc all) and rebuilt the drush registry (drush rr). To no avail. As the process is a bit erratic
>>>>>>> I interpret this as caused by the sequence of php file inclusions.
>>>>>>>
>>>>>>> We have certainly hit a wall here, and would appreciate any input as the migration is somewhat urgent to cmplete.
>>>>>>>
>>>>>>> Thank you in advance for your help.
>>>>>>>
>>>>>>> Michael
>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>> Full output below:
>>>>>>>
>>>>>>> $ drush updb
>>>>>>> Tripal_core        7204  Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>> Tripal_feature     7202  Adds the temporary tables used for loading GFF files.
>>>>>>> Tripal_pub         7202  Updates path of tripal_pub OBO to be relative.
>>>>>>> Tripal_stock       7201  Add materialized views
>>>>>>> Tripal_contact     7202  Updates path of tripal_contact OBO to be relative.
>>>>>>> Tripal_featuremap  7202  Fixes a typo when setting the default CV for the unittype_id field of the
>>>>>>>                           featuremap table.
>>>>>>> Do you wish to run all pending updates? (y/n): y
>>>>>>> PHP Fatal error:  Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>>>>>
>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install, line 409
>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>> 'all' cache was cleared in self [success]
>>>>>>> Finished performing updates. [ok]
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Jan 21, 2016, at 9:32 PM, Michael Dondrup wrote:
>>>>>>>
>>>>>>>> Hi Stephen,
>>>>>>>>
>>>>>>>> thank your for your response, I think we are getting closer to the core of the problem.
>>>>>>>> Do you think this might cause also the 'call to undefined function' error?
>>>>>>>>
>>>>>>>> Michael
>>>>>>>>
>>>>>>>> On Jan 21, 2016, at 8:00 PM, Stephen Ficklin wrote:
>>>>>>>>
>>>>>>>>> Hi Michael,
>>>>>>>>>
>>>>>>>>> When you started your upgrade did you have the search_path set for the postrgreSQL user?
>>>>>>>> Yes we had re-set the search path to public only.
>>>>>>>>
>>>>>>>>
>>>>>>>>> (Step 3 in upgrade procedue http://tripal.info/tutorials/v2.0/upgrade).  If so, then perhaps some of the tables that should be in the 'public' schema in your D6 site are in the 'chado' schema and they shouldn't be.
>>>>>>>> I think this is the case: The following tripal* tables are in chado in our D6 system:
>>>>>>>>
>>>>>>>> licebase=> \dt chado.tripal*
>>>>>>>>                List of relations
>>>>>>>> Schema |         Name         | Type  |  Owner
>>>>>>>> --------+----------------------+-------+----------
>>>>>>>> chado  | tripal_custom_tables | table | lb_admin
>>>>>>>> chado  | tripal_gff_temp      | table | lb_admin
>>>>>>>> chado  | tripal_jobs          | table | lb_admin
>>>>>>>> chado  | tripal_mviews        | table | lb_admin
>>>>>>>> chado  | tripal_obo_temp      | table | lb_admin
>>>>>>>> (5 rows)
>>>>>>>>
>>>>>>>> The following ones are in public
>>>>>>>>
>>>>>>>> licebase=> \dt public.tripal*
>>>>>>>>                    List of relations
>>>>>>>> Schema |             Name             | Type  |  Owner
>>>>>>>> --------+------------------------------+-------+----------
>>>>>>>> public | tripal_analysis              | table | lb_admin
>>>>>>>> public | tripal_analysis_blast        | table | lb_admin
>>>>>>>> public | tripal_bulk_loader           | table | lb_admin
>>>>>>>> public | tripal_bulk_loader_constants | table | lb_admin
>>>>>>>> public | tripal_bulk_loader_inserted  | table | lb_admin
>>>>>>>> public | tripal_bulk_loader_template  | table | lb_admin
>>>>>>>> public | tripal_cv_obo                | table | lb_admin
>>>>>>>> public | tripal_feature_relagg        | table | lb_admin
>>>>>>>> public | tripal_pub_import            | table | lb_admin
>>>>>>>> public | tripal_views                 | table | lb_admin
>>>>>>>> public | tripal_views_field           | table | lb_admin
>>>>>>>> public | tripal_views_handlers        | table | lb_admin
>>>>>>>> public | tripal_views_join            | table | lb_admin
>>>>>>>> (13 rows)
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> I do remember a bug at one point in one of our development versions that caused this.  If this is the case then it makes sense that you would have problems during the upgrade.   Do you have a backup of your D6 site database where you can look to see if those tables are in the 'chado' schema?
>>>>>>>> W are working on an identical copy, while the D6 Tripal1 system is still online and we have backups of each stage so we can start over. So I could just look it up in the
>>>>>>>> production system.
>>>>>>>>
>>>>>>>>
>>>>>>>>> If so, moving them to the 'public' schema and then retrying the upgrade may help.  If you do see some of these tables in the 'chado' schema but you're unsure if there are more that should also be moved feel free to send the list of tables in your 'chado' schema and I can let you know.
>>>>>>>> So should I first attempt move all those tripal* tables from chado to public? Funny enough this doesn't cause problems in the D6 system....
>>>>>>>>
>>>>>>>>
>>>>>>>>> Stephen
>>>>>>>>>
>>>>>>>>> On 1/21/2016 1:15 AM, Michael Dondrup wrote:
>>>>>>>>>> Hi,
>>>>>>>>>> we fixed the first problem somehow the tripal_custom_tables table was created in chado schema. I moved it
>>>>>>>>>> ALTER TABLE tripal_custom_tables SET SCHEMA public;
>>>>>>>>>>
>>>>>>>>>> Leaving me with this error:
>>>>>>>>>>
>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> This is weird because the function is certainly defined in tripal/tripal_cv/api/tripal_cv.api.inc:function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE)
>>>>>>>>>>
>>>>>>>>>> I have tried to drush cc all and even rebuilt the registry as described here: https://www.drupal.org/project/registry_rebuild
>>>>>>>>>>
>>>>>>>>>> But to no avail. Anybody else having this problem?
>>>>>>>>>>
>>>>>>>>>> I really appreciate your help.
>>>>>>>>>>
>>>>>>>>>> Michael
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Jan 20, 2016, at 2:17 PM, Michael Dondrup wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> we are doing a test-run of the D6->7 migration of our site including a Tripal update, following http://tripal.info/tutorials/v2.0/upgrade
>>>>>>>>>>>
>>>>>>>>>>> We are currently at step 14. Next, apply the Tripal updates: drush updatedb
>>>>>>>>>>>
>>>>>>>>>>> All core updates, views and ctools have been performed without error and no pending db updates were scheduled prior to this step.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>>>>>> does not exist
>>>>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>>>>       ^
>>>>>>>>>>>
>>>>>>>>>>> [...]
>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>
>>>>>>>>>>> I guess we have a fix for the first one, however that yields different errors:
>>>>>>>>>>>
>>>>>>>>>>> The table tripal_mviews exists but in the schema chado. I tried to set the search_path back:
>>>>>>>>>>> ALTER USER user SET search_path TO public, chado;
>>>>>>>>>>>
>>>>>>>>>>> However this yields other errors:
>>>>>>>>>>>
>>>>>>>>>>> Cannot add field tripal_custom_tables.mview_id: table doesn't exist. [error]
>>>>>>>>>>> [...]
>>>>>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install on line 449
>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install, line 449
>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> I searched and found http://sourceforge.net/p/gmod/mailman/message/32762105/ but that doesn't seem to fit.
>>>>>>>>>>>
>>>>>>>>>>> Best
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Michael Dondrup
>>>>>>>>>>> Researcher
>>>>>>>>>>> Sea Lice Research Centre
>>>>>>>>>>> Department of Informatics
>>>>>>>>>>> University of Bergen
>>>>>>>>>>> Thormøhlensgate 55, N-5008 Bergen,
>>>>>>>>>>> Norway
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Full output of drush updatedb first iteration:
>>>>>>>>>>>
>>>>>>>>>>> $ drush updatedb
>>>>>>>>>>> The following updates are pending:
>>>>>>>>>>>
>>>>>>>>>>> tripal_core module :
>>>>>>>>>>> 7200 -   Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table
>>>>>>>>>>> 7201 -   Fixes missing language for nodes and URL aliases. This may take awhile...
>>>>>>>>>>> 7202 -   Adds a tripal_token_formats table for custom page titles and URL paths
>>>>>>>>>>> 7203 -   Adds a tripal_toc table for customizing the table of contents on each Tripal page.
>>>>>>>>>>> 7204 -   Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>>>>>>
>>>>>>>>>>> tripal_organism module :
>>>>>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>>>>>
>>>>>>>>>>> tripal_cv module :
>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>
>>>>>>>>>>> tripal_contact module :
>>>>>>>>>>> 7200 -   This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
>>>>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>>>>> 7202 -   Updates path of tripal_contact OBO to be relative.
>>>>>>>>>>>
>>>>>>>>>>> tripal_bulk_loader module :
>>>>>>>>>>> 7200 -   Implements hook_update_N().   Update to 7.x-2.0  -Cast tripal_bulk_loader.template_id to int field
>>>>>>>>>>>
>>>>>>>>>>> tripal_library module :
>>>>>>>>>>> 7200 -   This is the required update for tripal_library when upgrading from Drupal core API 6.x.
>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>
>>>>>>>>>>> tripal_stock module :
>>>>>>>>>>> 7200 -   This is the required update for tripal_stock when upgrading from Drupal core API 6.x.
>>>>>>>>>>> 7201 -   Add materialized views
>>>>>>>>>>>
>>>>>>>>>>> tripal_project module :
>>>>>>>>>>> 7200 -   This is the required update for tripal_project when upgrading from Drupal core API 6.x.
>>>>>>>>>>>
>>>>>>>>>>> tripal_analysis module :
>>>>>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>
>>>>>>>>>>> tripal_featuremap module :
>>>>>>>>>>> 7200 -   This is the required update for tripal_featuremap when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>>>>> 7202 -   Fixes a typo when setting the default CV for the unittype_id field of the featuremap table.
>>>>>>>>>>>
>>>>>>>>>>> tripal_feature module :
>>>>>>>>>>> 7200 -   This is the required update for tripal_feature when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>> 7202 -   Adds the temporary tables used for loading GFF files.
>>>>>>>>>>>
>>>>>>>>>>> tripal_views module :
>>>>>>>>>>> 7200 -   Tripal Views Update for 7.x-2.0    - Add relationship_only field to tripal_views_join    - Add relationship_handler field to tripal_views_join
>>>>>>>>>>>
>>>>>>>>>>> tripal_pub module :
>>>>>>>>>>> 7202 -   Updates path of tripal_pub OBO to be relative.
>>>>>>>>>>>
>>>>>>>>>>> Performed update: tripal_feature_update_7200 [ok]
>>>>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>>>>>> does not exist
>>>>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>>>>       ^
>>>>>>>>>>> Performed update: tripal_feature_update_7201 [ok]
>>>>>>>>>>> Performed update: tripal_featuremap_update_7200 [ok]
>>>>>>>>>>> Performed update: tripal_featuremap_update_7201 [ok]
>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>
>>>>>>>>>>> Fatal error: Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>> Finished performing updates. [ok]
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>>>> Full output after setting search_path to public, chado
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>> [hidden email]
>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>> [hidden email]
>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-tripal mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Michael Dondrup-3
Here we go, sorry to bother again.
After enabling tripal_feature and most other tripal modules, when trying to access a feature I get:

PHP Fatal error:  Call to undefined function chado_get_node_title() in /home/licebase/d7/sites/all/modules/tripal/tripal_feature/includes/tripal_feature.chado_node.inc on line 738, referer: https://localhost/tracker?page=1

Best
Michael


On Jan 25, 2016, at 5:58 PM, Stephen Ficklin wrote:

> Wonderful!  Yes, those warnings will unfortunately appear.  But, after you delete the view integrations (Step 17) they should be rebuilt and that message should go away.  I have made note of these warnings in the the upgrade instructions.
>
> Thanks for reaching out when you had issues.
>
> Stephen
>
> On 1/25/2016 6:20 AM, Michael Dondrup wrote:
>> Hi,
>>
>> thank you again. It worked!
>>
>> The dbupdate has been applied using the updated code.  There was only one repeated warning.
>>
>> in updating tripal_views
>>  [site https://...] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store relationship for studyprop_feature => feature when you should be using tripal_views_joins.
>>
>> I think we should take another snapshot here and start activating tripal core modules and see how that goes.
>>
>> Best
>> Michael
>>
>>
>> ----------------------------------------------------------------------------------------------------------------------------------------------
>> Below I will list the commands for our reference:
>>
>> # ALTER USER user SET search_path TO public; just to be shure
>>
>> ## applied taxonomy patch, but didn't start core update from scratch becasue we didn't have taxonomy errors
>>
>> ### starting from Snapshot step_12
>>
>> ## moved misplaced tables from chado to public in psql
>>
>> ALTER table chado.tripal_custom_tables set schema public;
>> ALTER table chado.tripal_gff_temp set schema public;
>> ALTER table chado.tripal_jobs set schema public;
>> ALTER table chado.tripal_mviews set schema public;
>> ALTER table chado.tripal_obo_temp set schema public;
>>
>>
>> ### Step 13.
>> drush pm-download views ctools
>> drush updatedb
>>
>> drush pm-enable ctools views views_ui
>>
>> ## all OK Snapshot taken step_13
>>
>> ### Step 14. modified to get latest beta
>>
>> cd sites/all/modules
>> git clone https://github.com/tripal/tripal.git -b 7.x-2.1-beta2
>> # warning: Remote branch 7.x-2.1-beta2 not found in upstream origin, using HEAD instead
>> cd tripal/
>> ## 7.x-2.1-beta2 is a tag
>> git checkout 7.x-2.1-beta2
>>
>> ### Step 15:
>> drush updatedb
>> ## all ok
>>
>> ### Step 16:
>>
>> drush pm-enable tripal_core
>> ## all ok
>> drush pm-enable tripal_views
>>
>> # repeated many times
>> # [site https://...] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store
>> # relationship for studyprop_feature => feature when you should be using tripal_views_joins.
>>
>> ### Step 17: Administration -> Tripal -> Views Integration -> click 'Delete All Integrations'
>> # Successfully deleted all views integration.
>> #Successfully rebuilt default Tripal Views Integrations
>>
>> ## Changed tripal_core.info to avoid update warnings
>>> version = 7.x-2.1-beta2
>>
>>
>> On Jan 24, 2016, at 11:17 AM, Michael Dondrup wrote:
>>
>>> Hi Stephen,
>>> thank you so much for the quick response. I need to get our sysadmin involved to revert the database
>>> to the correct snapshot. I hope I will be ready testing before the afternoon on monday.
>>>
>>> Michael
>>>
>>> On Jan 23, 2016, at 9:11 PM, Stephen Ficklin wrote:
>>>
>>>> Hi Michael,
>>>>
>>>> I found one irritating bug that should have been fixed for the beta1 release. I've fixed it but Drupal.org won't let me redo the release to include the fix, so I had to issue a new beta2 release.  Also, I'm not sure the command I gave you below to download Tripal will work, and I can't test it to make sure until Drupal creates the files.  So use this instead:
>>>>
>>>> git clone [hidden email]:tripal/tripal.git -b 7.x-2.1-beta2
>>>>
>>>> Stephen
>>>>
>>>> On 1/23/2016 11:02 AM, Stephen Ficklin wrote:
>>>>> Hi Michael,
>>>>>
>>>>> The fixes are ready.  I have also adjusted the upgrade documentation to add a patch for a taxonomy bug that seems to occur for some people during upgrade.  I added a new step #10 to the upgrade documentation http://tripal.info/tutorials/v2.0/upgrade.    I also just released Tripal v2.1-beta1.  This is a precursor for our full Tripal v2.1 release (which will include support for Chado v1.3).
>>>>>
>>>>> So, in step #14 when it asks you download Tripal use this command instead
>>>>>
>>>>> drush pm-download tripal 7.x-2.1-beta1
>>>>>
>>>>> Drupal only rebuilds its releases at the end of the day so this beta release should be available tomorrow.
>>>>>
>>>>> I have tested an upgrade of Drupal 6 / Tripal v1 to Drupal 7 / Tripal v2 and it worked just fine without problems using this new beta1 version.
>>>>>
>>>>> Let me know if you have issues.
>>>>>
>>>>> Stephen
>>>>>
>>>>>
>>>>> On 1/22/2016 10:26 AM, Michael Dondrup wrote:
>>>>>> Hi Stephen,
>>>>>>
>>>>>> That would be great, we will just revert to the state directly after updating clean drupal core
>>>>>> next week.
>>>>>> Will php 5.3.3 and drush 6.7.0 be ok?
>>>>>>
>>>>>> Michael
>>>>>>
>>>>>>
>>>>>> On Jan 22, 2016, at 6:31 PM, Stephen Ficklin wrote:
>>>>>>
>>>>>>> Hi Michael,
>>>>>>>
>>>>>>> I believe I understand what the problem is.   I'm going to add a fix to Tripal v2.x (the development branch) and let you know when it's ready.  Can you use the development branch for testing your upgrade?  We're very close to releasing v2.1 so it should be stable enough to use.
>>>>>>>
>>>>>>> Stephen
>>>>>>>
>>>>>>> On 1/22/2016 2:39 AM, Michael Dondrup wrote:
>>>>>>>> Hi,
>>>>>>>> we are still getting the 'undefined function errors' for functions that are in reality defined in the code of tripal:
>>>>>>>> e.g. tripal_add_mview() or tripal_insert_obo(). These functions sometimes change erratically throughout the process.
>>>>>>>> We were suspecting the drush version as we were initially using drush 5.7, we have therefore tested with other
>>>>>>>> versions: 6.4 (as recommended in the documentation), 6.0, 6.7 (latest stable 6), 5.5.9. We also tried drush 7 branches, but
>>>>>>>> these don't recognize a drupal site.
>>>>>>>>
>>>>>>>> Drush install via composer, php version is PHP 5.3.3
>>>>>>>>
>>>>>>>> Each time we cleared the cache (drush cc all) and rebuilt the drush registry (drush rr). To no avail. As the process is a bit erratic
>>>>>>>> I interpret this as caused by the sequence of php file inclusions.
>>>>>>>>
>>>>>>>> We have certainly hit a wall here, and would appreciate any input as the migration is somewhat urgent to cmplete.
>>>>>>>>
>>>>>>>> Thank you in advance for your help.
>>>>>>>>
>>>>>>>> Michael
>>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>> Full output below:
>>>>>>>>
>>>>>>>> $ drush updb
>>>>>>>> Tripal_core        7204  Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>>> Tripal_feature     7202  Adds the temporary tables used for loading GFF files.
>>>>>>>> Tripal_pub         7202  Updates path of tripal_pub OBO to be relative.
>>>>>>>> Tripal_stock       7201  Add materialized views
>>>>>>>> Tripal_contact     7202  Updates path of tripal_contact OBO to be relative.
>>>>>>>> Tripal_featuremap  7202  Fixes a typo when setting the default CV for the unittype_id field of the
>>>>>>>>                          featuremap table.
>>>>>>>> Do you wish to run all pending updates? (y/n): y
>>>>>>>> PHP Fatal error:  Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>>>>>>
>>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>>>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install, line 409
>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>> 'all' cache was cleared in self [success]
>>>>>>>> Finished performing updates. [ok]
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Jan 21, 2016, at 9:32 PM, Michael Dondrup wrote:
>>>>>>>>
>>>>>>>>> Hi Stephen,
>>>>>>>>>
>>>>>>>>> thank your for your response, I think we are getting closer to the core of the problem.
>>>>>>>>> Do you think this might cause also the 'call to undefined function' error?
>>>>>>>>>
>>>>>>>>> Michael
>>>>>>>>>
>>>>>>>>> On Jan 21, 2016, at 8:00 PM, Stephen Ficklin wrote:
>>>>>>>>>
>>>>>>>>>> Hi Michael,
>>>>>>>>>>
>>>>>>>>>> When you started your upgrade did you have the search_path set for the postrgreSQL user?
>>>>>>>>> Yes we had re-set the search path to public only.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> (Step 3 in upgrade procedue http://tripal.info/tutorials/v2.0/upgrade).  If so, then perhaps some of the tables that should be in the 'public' schema in your D6 site are in the 'chado' schema and they shouldn't be.
>>>>>>>>> I think this is the case: The following tripal* tables are in chado in our D6 system:
>>>>>>>>>
>>>>>>>>> licebase=> \dt chado.tripal*
>>>>>>>>>               List of relations
>>>>>>>>> Schema |         Name         | Type  |  Owner
>>>>>>>>> --------+----------------------+-------+----------
>>>>>>>>> chado  | tripal_custom_tables | table | lb_admin
>>>>>>>>> chado  | tripal_gff_temp      | table | lb_admin
>>>>>>>>> chado  | tripal_jobs          | table | lb_admin
>>>>>>>>> chado  | tripal_mviews        | table | lb_admin
>>>>>>>>> chado  | tripal_obo_temp      | table | lb_admin
>>>>>>>>> (5 rows)
>>>>>>>>>
>>>>>>>>> The following ones are in public
>>>>>>>>>
>>>>>>>>> licebase=> \dt public.tripal*
>>>>>>>>>                   List of relations
>>>>>>>>> Schema |             Name             | Type  |  Owner
>>>>>>>>> --------+------------------------------+-------+----------
>>>>>>>>> public | tripal_analysis              | table | lb_admin
>>>>>>>>> public | tripal_analysis_blast        | table | lb_admin
>>>>>>>>> public | tripal_bulk_loader           | table | lb_admin
>>>>>>>>> public | tripal_bulk_loader_constants | table | lb_admin
>>>>>>>>> public | tripal_bulk_loader_inserted  | table | lb_admin
>>>>>>>>> public | tripal_bulk_loader_template  | table | lb_admin
>>>>>>>>> public | tripal_cv_obo                | table | lb_admin
>>>>>>>>> public | tripal_feature_relagg        | table | lb_admin
>>>>>>>>> public | tripal_pub_import            | table | lb_admin
>>>>>>>>> public | tripal_views                 | table | lb_admin
>>>>>>>>> public | tripal_views_field           | table | lb_admin
>>>>>>>>> public | tripal_views_handlers        | table | lb_admin
>>>>>>>>> public | tripal_views_join            | table | lb_admin
>>>>>>>>> (13 rows)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> I do remember a bug at one point in one of our development versions that caused this.  If this is the case then it makes sense that you would have problems during the upgrade.   Do you have a backup of your D6 site database where you can look to see if those tables are in the 'chado' schema?
>>>>>>>>> W are working on an identical copy, while the D6 Tripal1 system is still online and we have backups of each stage so we can start over. So I could just look it up in the
>>>>>>>>> production system.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> If so, moving them to the 'public' schema and then retrying the upgrade may help.  If you do see some of these tables in the 'chado' schema but you're unsure if there are more that should also be moved feel free to send the list of tables in your 'chado' schema and I can let you know.
>>>>>>>>> So should I first attempt move all those tripal* tables from chado to public? Funny enough this doesn't cause problems in the D6 system....
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Stephen
>>>>>>>>>>
>>>>>>>>>> On 1/21/2016 1:15 AM, Michael Dondrup wrote:
>>>>>>>>>>> Hi,
>>>>>>>>>>> we fixed the first problem somehow the tripal_custom_tables table was created in chado schema. I moved it
>>>>>>>>>>> ALTER TABLE tripal_custom_tables SET SCHEMA public;
>>>>>>>>>>>
>>>>>>>>>>> Leaving me with this error:
>>>>>>>>>>>
>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> This is weird because the function is certainly defined in tripal/tripal_cv/api/tripal_cv.api.inc:function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE)
>>>>>>>>>>>
>>>>>>>>>>> I have tried to drush cc all and even rebuilt the registry as described here: https://www.drupal.org/project/registry_rebuild
>>>>>>>>>>>
>>>>>>>>>>> But to no avail. Anybody else having this problem?
>>>>>>>>>>>
>>>>>>>>>>> I really appreciate your help.
>>>>>>>>>>>
>>>>>>>>>>> Michael
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Jan 20, 2016, at 2:17 PM, Michael Dondrup wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi,
>>>>>>>>>>>>
>>>>>>>>>>>> we are doing a test-run of the D6->7 migration of our site including a Tripal update, following http://tripal.info/tutorials/v2.0/upgrade
>>>>>>>>>>>>
>>>>>>>>>>>> We are currently at step 14. Next, apply the Tripal updates: drush updatedb
>>>>>>>>>>>>
>>>>>>>>>>>> All core updates, views and ctools have been performed without error and no pending db updates were scheduled prior to this step.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>>>>>>> does not exist
>>>>>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>>>>>      ^
>>>>>>>>>>>>
>>>>>>>>>>>> [...]
>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>
>>>>>>>>>>>> I guess we have a fix for the first one, however that yields different errors:
>>>>>>>>>>>>
>>>>>>>>>>>> The table tripal_mviews exists but in the schema chado. I tried to set the search_path back:
>>>>>>>>>>>> ALTER USER user SET search_path TO public, chado;
>>>>>>>>>>>>
>>>>>>>>>>>> However this yields other errors:
>>>>>>>>>>>>
>>>>>>>>>>>> Cannot add field tripal_custom_tables.mview_id: table doesn't exist. [error]
>>>>>>>>>>>> [...]
>>>>>>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install on line 449
>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install, line 449
>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> I searched and found http://sourceforge.net/p/gmod/mailman/message/32762105/ but that doesn't seem to fit.
>>>>>>>>>>>>
>>>>>>>>>>>> Best
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Michael Dondrup
>>>>>>>>>>>> Researcher
>>>>>>>>>>>> Sea Lice Research Centre
>>>>>>>>>>>> Department of Informatics
>>>>>>>>>>>> University of Bergen
>>>>>>>>>>>> Thormøhlensgate 55, N-5008 Bergen,
>>>>>>>>>>>> Norway
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Full output of drush updatedb first iteration:
>>>>>>>>>>>>
>>>>>>>>>>>> $ drush updatedb
>>>>>>>>>>>> The following updates are pending:
>>>>>>>>>>>>
>>>>>>>>>>>> tripal_core module :
>>>>>>>>>>>> 7200 -   Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table
>>>>>>>>>>>> 7201 -   Fixes missing language for nodes and URL aliases. This may take awhile...
>>>>>>>>>>>> 7202 -   Adds a tripal_token_formats table for custom page titles and URL paths
>>>>>>>>>>>> 7203 -   Adds a tripal_toc table for customizing the table of contents on each Tripal page.
>>>>>>>>>>>> 7204 -   Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>>>>>>>
>>>>>>>>>>>> tripal_organism module :
>>>>>>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>
>>>>>>>>>>>> tripal_cv module :
>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>
>>>>>>>>>>>> tripal_contact module :
>>>>>>>>>>>> 7200 -   This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
>>>>>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>>>>>> 7202 -   Updates path of tripal_contact OBO to be relative.
>>>>>>>>>>>>
>>>>>>>>>>>> tripal_bulk_loader module :
>>>>>>>>>>>> 7200 -   Implements hook_update_N().   Update to 7.x-2.0  -Cast tripal_bulk_loader.template_id to int field
>>>>>>>>>>>>
>>>>>>>>>>>> tripal_library module :
>>>>>>>>>>>> 7200 -   This is the required update for tripal_library when upgrading from Drupal core API 6.x.
>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>
>>>>>>>>>>>> tripal_stock module :
>>>>>>>>>>>> 7200 -   This is the required update for tripal_stock when upgrading from Drupal core API 6.x.
>>>>>>>>>>>> 7201 -   Add materialized views
>>>>>>>>>>>>
>>>>>>>>>>>> tripal_project module :
>>>>>>>>>>>> 7200 -   This is the required update for tripal_project when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>
>>>>>>>>>>>> tripal_analysis module :
>>>>>>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>
>>>>>>>>>>>> tripal_featuremap module :
>>>>>>>>>>>> 7200 -   This is the required update for tripal_featuremap when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>>>>>> 7202 -   Fixes a typo when setting the default CV for the unittype_id field of the featuremap table.
>>>>>>>>>>>>
>>>>>>>>>>>> tripal_feature module :
>>>>>>>>>>>> 7200 -   This is the required update for tripal_feature when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>> 7202 -   Adds the temporary tables used for loading GFF files.
>>>>>>>>>>>>
>>>>>>>>>>>> tripal_views module :
>>>>>>>>>>>> 7200 -   Tripal Views Update for 7.x-2.0    - Add relationship_only field to tripal_views_join    - Add relationship_handler field to tripal_views_join
>>>>>>>>>>>>
>>>>>>>>>>>> tripal_pub module :
>>>>>>>>>>>> 7202 -   Updates path of tripal_pub OBO to be relative.
>>>>>>>>>>>>
>>>>>>>>>>>> Performed update: tripal_feature_update_7200 [ok]
>>>>>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>>>>>>> does not exist
>>>>>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>>>>>      ^
>>>>>>>>>>>> Performed update: tripal_feature_update_7201 [ok]
>>>>>>>>>>>> Performed update: tripal_featuremap_update_7200 [ok]
>>>>>>>>>>>> Performed update: tripal_featuremap_update_7201 [ok]
>>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>
>>>>>>>>>>>> Fatal error: Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>> Finished performing updates. [ok]
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>>>>> Full output after setting search_path to public, chado
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>> [hidden email]
>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>> _______________________________________________
>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>> [hidden email]
>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Stephen Ficklin-2
Hi Michael,

No need to apologize.   This was my mistake. I made a typo in the fix I
made to get you passed the upgrade problems.  I fixed it, tested on my
end and seems to be fine.  Please pull the most recent version of the
development code from the git repository and you should have the fix.

Please let me know if you have additional issues.

Stephen

On 1/25/2016 1:32 PM, Michael Dondrup wrote:

> Here we go, sorry to bother again.
> After enabling tripal_feature and most other tripal modules, when trying to access a feature I get:
>
> PHP Fatal error:  Call to undefined function chado_get_node_title() in /home/licebase/d7/sites/all/modules/tripal/tripal_feature/includes/tripal_feature.chado_node.inc on line 738, referer: https://localhost/tracker?page=1
>
> Best
> Michael
>
>
> On Jan 25, 2016, at 5:58 PM, Stephen Ficklin wrote:
>
>> Wonderful!  Yes, those warnings will unfortunately appear.  But, after you delete the view integrations (Step 17) they should be rebuilt and that message should go away.  I have made note of these warnings in the the upgrade instructions.
>>
>> Thanks for reaching out when you had issues.
>>
>> Stephen
>>
>> On 1/25/2016 6:20 AM, Michael Dondrup wrote:
>>> Hi,
>>>
>>> thank you again. It worked!
>>>
>>> The dbupdate has been applied using the updated code.  There was only one repeated warning.
>>>
>>> in updating tripal_views
>>>   [site https://...] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store relationship for studyprop_feature => feature when you should be using tripal_views_joins.
>>>
>>> I think we should take another snapshot here and start activating tripal core modules and see how that goes.
>>>
>>> Best
>>> Michael
>>>
>>>
>>> ----------------------------------------------------------------------------------------------------------------------------------------------
>>> Below I will list the commands for our reference:
>>>
>>> # ALTER USER user SET search_path TO public; just to be shure
>>>
>>> ## applied taxonomy patch, but didn't start core update from scratch becasue we didn't have taxonomy errors
>>>
>>> ### starting from Snapshot step_12
>>>
>>> ## moved misplaced tables from chado to public in psql
>>>
>>> ALTER table chado.tripal_custom_tables set schema public;
>>> ALTER table chado.tripal_gff_temp set schema public;
>>> ALTER table chado.tripal_jobs set schema public;
>>> ALTER table chado.tripal_mviews set schema public;
>>> ALTER table chado.tripal_obo_temp set schema public;
>>>
>>>
>>> ### Step 13.
>>> drush pm-download views ctools
>>> drush updatedb
>>>
>>> drush pm-enable ctools views views_ui
>>>
>>> ## all OK Snapshot taken step_13
>>>
>>> ### Step 14. modified to get latest beta
>>>
>>> cd sites/all/modules
>>> git clone https://github.com/tripal/tripal.git -b 7.x-2.1-beta2
>>> # warning: Remote branch 7.x-2.1-beta2 not found in upstream origin, using HEAD instead
>>> cd tripal/
>>> ## 7.x-2.1-beta2 is a tag
>>> git checkout 7.x-2.1-beta2
>>>
>>> ### Step 15:
>>> drush updatedb
>>> ## all ok
>>>
>>> ### Step 16:
>>>
>>> drush pm-enable tripal_core
>>> ## all ok
>>> drush pm-enable tripal_views
>>>
>>> # repeated many times
>>> # [site https://...] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store
>>> # relationship for studyprop_feature => feature when you should be using tripal_views_joins.
>>>
>>> ### Step 17: Administration -> Tripal -> Views Integration -> click 'Delete All Integrations'
>>> # Successfully deleted all views integration.
>>> #Successfully rebuilt default Tripal Views Integrations
>>>
>>> ## Changed tripal_core.info to avoid update warnings
>>>> version = 7.x-2.1-beta2
>>>
>>> On Jan 24, 2016, at 11:17 AM, Michael Dondrup wrote:
>>>
>>>> Hi Stephen,
>>>> thank you so much for the quick response. I need to get our sysadmin involved to revert the database
>>>> to the correct snapshot. I hope I will be ready testing before the afternoon on monday.
>>>>
>>>> Michael
>>>>
>>>> On Jan 23, 2016, at 9:11 PM, Stephen Ficklin wrote:
>>>>
>>>>> Hi Michael,
>>>>>
>>>>> I found one irritating bug that should have been fixed for the beta1 release. I've fixed it but Drupal.org won't let me redo the release to include the fix, so I had to issue a new beta2 release.  Also, I'm not sure the command I gave you below to download Tripal will work, and I can't test it to make sure until Drupal creates the files.  So use this instead:
>>>>>
>>>>> git clone [hidden email]:tripal/tripal.git -b 7.x-2.1-beta2
>>>>>
>>>>> Stephen
>>>>>
>>>>> On 1/23/2016 11:02 AM, Stephen Ficklin wrote:
>>>>>> Hi Michael,
>>>>>>
>>>>>> The fixes are ready.  I have also adjusted the upgrade documentation to add a patch for a taxonomy bug that seems to occur for some people during upgrade.  I added a new step #10 to the upgrade documentation http://tripal.info/tutorials/v2.0/upgrade.    I also just released Tripal v2.1-beta1.  This is a precursor for our full Tripal v2.1 release (which will include support for Chado v1.3).
>>>>>>
>>>>>> So, in step #14 when it asks you download Tripal use this command instead
>>>>>>
>>>>>> drush pm-download tripal 7.x-2.1-beta1
>>>>>>
>>>>>> Drupal only rebuilds its releases at the end of the day so this beta release should be available tomorrow.
>>>>>>
>>>>>> I have tested an upgrade of Drupal 6 / Tripal v1 to Drupal 7 / Tripal v2 and it worked just fine without problems using this new beta1 version.
>>>>>>
>>>>>> Let me know if you have issues.
>>>>>>
>>>>>> Stephen
>>>>>>
>>>>>>
>>>>>> On 1/22/2016 10:26 AM, Michael Dondrup wrote:
>>>>>>> Hi Stephen,
>>>>>>>
>>>>>>> That would be great, we will just revert to the state directly after updating clean drupal core
>>>>>>> next week.
>>>>>>> Will php 5.3.3 and drush 6.7.0 be ok?
>>>>>>>
>>>>>>> Michael
>>>>>>>
>>>>>>>
>>>>>>> On Jan 22, 2016, at 6:31 PM, Stephen Ficklin wrote:
>>>>>>>
>>>>>>>> Hi Michael,
>>>>>>>>
>>>>>>>> I believe I understand what the problem is.   I'm going to add a fix to Tripal v2.x (the development branch) and let you know when it's ready.  Can you use the development branch for testing your upgrade?  We're very close to releasing v2.1 so it should be stable enough to use.
>>>>>>>>
>>>>>>>> Stephen
>>>>>>>>
>>>>>>>> On 1/22/2016 2:39 AM, Michael Dondrup wrote:
>>>>>>>>> Hi,
>>>>>>>>> we are still getting the 'undefined function errors' for functions that are in reality defined in the code of tripal:
>>>>>>>>> e.g. tripal_add_mview() or tripal_insert_obo(). These functions sometimes change erratically throughout the process.
>>>>>>>>> We were suspecting the drush version as we were initially using drush 5.7, we have therefore tested with other
>>>>>>>>> versions: 6.4 (as recommended in the documentation), 6.0, 6.7 (latest stable 6), 5.5.9. We also tried drush 7 branches, but
>>>>>>>>> these don't recognize a drupal site.
>>>>>>>>>
>>>>>>>>> Drush install via composer, php version is PHP 5.3.3
>>>>>>>>>
>>>>>>>>> Each time we cleared the cache (drush cc all) and rebuilt the drush registry (drush rr). To no avail. As the process is a bit erratic
>>>>>>>>> I interpret this as caused by the sequence of php file inclusions.
>>>>>>>>>
>>>>>>>>> We have certainly hit a wall here, and would appreciate any input as the migration is somewhat urgent to cmplete.
>>>>>>>>>
>>>>>>>>> Thank you in advance for your help.
>>>>>>>>>
>>>>>>>>> Michael
>>>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>> Full output below:
>>>>>>>>>
>>>>>>>>> $ drush updb
>>>>>>>>> Tripal_core        7204  Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>>>> Tripal_feature     7202  Adds the temporary tables used for loading GFF files.
>>>>>>>>> Tripal_pub         7202  Updates path of tripal_pub OBO to be relative.
>>>>>>>>> Tripal_stock       7201  Add materialized views
>>>>>>>>> Tripal_contact     7202  Updates path of tripal_contact OBO to be relative.
>>>>>>>>> Tripal_featuremap  7202  Fixes a typo when setting the default CV for the unittype_id field of the
>>>>>>>>>                           featuremap table.
>>>>>>>>> Do you wish to run all pending updates? (y/n): y
>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>>>>>>>
>>>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install, line 409
>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>> 'all' cache was cleared in self [success]
>>>>>>>>> Finished performing updates. [ok]
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Jan 21, 2016, at 9:32 PM, Michael Dondrup wrote:
>>>>>>>>>
>>>>>>>>>> Hi Stephen,
>>>>>>>>>>
>>>>>>>>>> thank your for your response, I think we are getting closer to the core of the problem.
>>>>>>>>>> Do you think this might cause also the 'call to undefined function' error?
>>>>>>>>>>
>>>>>>>>>> Michael
>>>>>>>>>>
>>>>>>>>>> On Jan 21, 2016, at 8:00 PM, Stephen Ficklin wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Michael,
>>>>>>>>>>>
>>>>>>>>>>> When you started your upgrade did you have the search_path set for the postrgreSQL user?
>>>>>>>>>> Yes we had re-set the search path to public only.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> (Step 3 in upgrade procedue http://tripal.info/tutorials/v2.0/upgrade).  If so, then perhaps some of the tables that should be in the 'public' schema in your D6 site are in the 'chado' schema and they shouldn't be.
>>>>>>>>>> I think this is the case: The following tripal* tables are in chado in our D6 system:
>>>>>>>>>>
>>>>>>>>>> licebase=> \dt chado.tripal*
>>>>>>>>>>                List of relations
>>>>>>>>>> Schema |         Name         | Type  |  Owner
>>>>>>>>>> --------+----------------------+-------+----------
>>>>>>>>>> chado  | tripal_custom_tables | table | lb_admin
>>>>>>>>>> chado  | tripal_gff_temp      | table | lb_admin
>>>>>>>>>> chado  | tripal_jobs          | table | lb_admin
>>>>>>>>>> chado  | tripal_mviews        | table | lb_admin
>>>>>>>>>> chado  | tripal_obo_temp      | table | lb_admin
>>>>>>>>>> (5 rows)
>>>>>>>>>>
>>>>>>>>>> The following ones are in public
>>>>>>>>>>
>>>>>>>>>> licebase=> \dt public.tripal*
>>>>>>>>>>                    List of relations
>>>>>>>>>> Schema |             Name             | Type  |  Owner
>>>>>>>>>> --------+------------------------------+-------+----------
>>>>>>>>>> public | tripal_analysis              | table | lb_admin
>>>>>>>>>> public | tripal_analysis_blast        | table | lb_admin
>>>>>>>>>> public | tripal_bulk_loader           | table | lb_admin
>>>>>>>>>> public | tripal_bulk_loader_constants | table | lb_admin
>>>>>>>>>> public | tripal_bulk_loader_inserted  | table | lb_admin
>>>>>>>>>> public | tripal_bulk_loader_template  | table | lb_admin
>>>>>>>>>> public | tripal_cv_obo                | table | lb_admin
>>>>>>>>>> public | tripal_feature_relagg        | table | lb_admin
>>>>>>>>>> public | tripal_pub_import            | table | lb_admin
>>>>>>>>>> public | tripal_views                 | table | lb_admin
>>>>>>>>>> public | tripal_views_field           | table | lb_admin
>>>>>>>>>> public | tripal_views_handlers        | table | lb_admin
>>>>>>>>>> public | tripal_views_join            | table | lb_admin
>>>>>>>>>> (13 rows)
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> I do remember a bug at one point in one of our development versions that caused this.  If this is the case then it makes sense that you would have problems during the upgrade.   Do you have a backup of your D6 site database where you can look to see if those tables are in the 'chado' schema?
>>>>>>>>>> W are working on an identical copy, while the D6 Tripal1 system is still online and we have backups of each stage so we can start over. So I could just look it up in the
>>>>>>>>>> production system.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> If so, moving them to the 'public' schema and then retrying the upgrade may help.  If you do see some of these tables in the 'chado' schema but you're unsure if there are more that should also be moved feel free to send the list of tables in your 'chado' schema and I can let you know.
>>>>>>>>>> So should I first attempt move all those tripal* tables from chado to public? Funny enough this doesn't cause problems in the D6 system....
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Stephen
>>>>>>>>>>>
>>>>>>>>>>> On 1/21/2016 1:15 AM, Michael Dondrup wrote:
>>>>>>>>>>>> Hi,
>>>>>>>>>>>> we fixed the first problem somehow the tripal_custom_tables table was created in chado schema. I moved it
>>>>>>>>>>>> ALTER TABLE tripal_custom_tables SET SCHEMA public;
>>>>>>>>>>>>
>>>>>>>>>>>> Leaving me with this error:
>>>>>>>>>>>>
>>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> This is weird because the function is certainly defined in tripal/tripal_cv/api/tripal_cv.api.inc:function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE)
>>>>>>>>>>>>
>>>>>>>>>>>> I have tried to drush cc all and even rebuilt the registry as described here: https://www.drupal.org/project/registry_rebuild
>>>>>>>>>>>>
>>>>>>>>>>>> But to no avail. Anybody else having this problem?
>>>>>>>>>>>>
>>>>>>>>>>>> I really appreciate your help.
>>>>>>>>>>>>
>>>>>>>>>>>> Michael
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Jan 20, 2016, at 2:17 PM, Michael Dondrup wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>
>>>>>>>>>>>>> we are doing a test-run of the D6->7 migration of our site including a Tripal update, following http://tripal.info/tutorials/v2.0/upgrade
>>>>>>>>>>>>>
>>>>>>>>>>>>> We are currently at step 14. Next, apply the Tripal updates: drush updatedb
>>>>>>>>>>>>>
>>>>>>>>>>>>> All core updates, views and ctools have been performed without error and no pending db updates were scheduled prior to this step.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>>>>>>>> does not exist
>>>>>>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>>>>>>       ^
>>>>>>>>>>>>>
>>>>>>>>>>>>> [...]
>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>>
>>>>>>>>>>>>> I guess we have a fix for the first one, however that yields different errors:
>>>>>>>>>>>>>
>>>>>>>>>>>>> The table tripal_mviews exists but in the schema chado. I tried to set the search_path back:
>>>>>>>>>>>>> ALTER USER user SET search_path TO public, chado;
>>>>>>>>>>>>>
>>>>>>>>>>>>> However this yields other errors:
>>>>>>>>>>>>>
>>>>>>>>>>>>> Cannot add field tripal_custom_tables.mview_id: table doesn't exist. [error]
>>>>>>>>>>>>> [...]
>>>>>>>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install on line 449
>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install, line 449
>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> I searched and found http://sourceforge.net/p/gmod/mailman/message/32762105/ but that doesn't seem to fit.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Best
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Michael Dondrup
>>>>>>>>>>>>> Researcher
>>>>>>>>>>>>> Sea Lice Research Centre
>>>>>>>>>>>>> Department of Informatics
>>>>>>>>>>>>> University of Bergen
>>>>>>>>>>>>> Thormøhlensgate 55, N-5008 Bergen,
>>>>>>>>>>>>> Norway
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Full output of drush updatedb first iteration:
>>>>>>>>>>>>>
>>>>>>>>>>>>> $ drush updatedb
>>>>>>>>>>>>> The following updates are pending:
>>>>>>>>>>>>>
>>>>>>>>>>>>> tripal_core module :
>>>>>>>>>>>>> 7200 -   Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table
>>>>>>>>>>>>> 7201 -   Fixes missing language for nodes and URL aliases. This may take awhile...
>>>>>>>>>>>>> 7202 -   Adds a tripal_token_formats table for custom page titles and URL paths
>>>>>>>>>>>>> 7203 -   Adds a tripal_toc table for customizing the table of contents on each Tripal page.
>>>>>>>>>>>>> 7204 -   Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>>>>>>>>
>>>>>>>>>>>>> tripal_organism module :
>>>>>>>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>
>>>>>>>>>>>>> tripal_cv module :
>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>
>>>>>>>>>>>>> tripal_contact module :
>>>>>>>>>>>>> 7200 -   This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>>>>>>> 7202 -   Updates path of tripal_contact OBO to be relative.
>>>>>>>>>>>>>
>>>>>>>>>>>>> tripal_bulk_loader module :
>>>>>>>>>>>>> 7200 -   Implements hook_update_N().   Update to 7.x-2.0  -Cast tripal_bulk_loader.template_id to int field
>>>>>>>>>>>>>
>>>>>>>>>>>>> tripal_library module :
>>>>>>>>>>>>> 7200 -   This is the required update for tripal_library when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>
>>>>>>>>>>>>> tripal_stock module :
>>>>>>>>>>>>> 7200 -   This is the required update for tripal_stock when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>> 7201 -   Add materialized views
>>>>>>>>>>>>>
>>>>>>>>>>>>> tripal_project module :
>>>>>>>>>>>>> 7200 -   This is the required update for tripal_project when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>
>>>>>>>>>>>>> tripal_analysis module :
>>>>>>>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>
>>>>>>>>>>>>> tripal_featuremap module :
>>>>>>>>>>>>> 7200 -   This is the required update for tripal_featuremap when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>>>>>>> 7202 -   Fixes a typo when setting the default CV for the unittype_id field of the featuremap table.
>>>>>>>>>>>>>
>>>>>>>>>>>>> tripal_feature module :
>>>>>>>>>>>>> 7200 -   This is the required update for tripal_feature when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>> 7202 -   Adds the temporary tables used for loading GFF files.
>>>>>>>>>>>>>
>>>>>>>>>>>>> tripal_views module :
>>>>>>>>>>>>> 7200 -   Tripal Views Update for 7.x-2.0    - Add relationship_only field to tripal_views_join    - Add relationship_handler field to tripal_views_join
>>>>>>>>>>>>>
>>>>>>>>>>>>> tripal_pub module :
>>>>>>>>>>>>> 7202 -   Updates path of tripal_pub OBO to be relative.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Performed update: tripal_feature_update_7200 [ok]
>>>>>>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>>>>>>>> does not exist
>>>>>>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>>>>>>       ^
>>>>>>>>>>>>> Performed update: tripal_feature_update_7201 [ok]
>>>>>>>>>>>>> Performed update: tripal_featuremap_update_7200 [ok]
>>>>>>>>>>>>> Performed update: tripal_featuremap_update_7201 [ok]
>>>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>>
>>>>>>>>>>>>> Fatal error: Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>> Finished performing updates. [ok]
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>>>>>> Full output after setting search_path to public, chado
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>> [hidden email]
>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Michael Dondrup-3
Hi,

I pulled the latest 7.x-2.1-beta2 but the error is still the same.

Michael

On Jan 26, 2016, at 2:12 AM, Stephen Ficklin wrote:

> Hi Michael,
>
> No need to apologize.   This was my mistake. I made a typo in the fix I made to get you passed the upgrade problems.  I fixed it, tested on my end and seems to be fine.  Please pull the most recent version of the development code from the git repository and you should have the fix.
>
> Please let me know if you have additional issues.
>
> Stephen
>
> On 1/25/2016 1:32 PM, Michael Dondrup wrote:
>> Here we go, sorry to bother again.
>> After enabling tripal_feature and most other tripal modules, when trying to access a feature I get:
>>
>> PHP Fatal error:  Call to undefined function chado_get_node_title() in /home/licebase/d7/sites/all/modules/tripal/tripal_feature/includes/tripal_feature.chado_node.inc on line 738, referer: https://localhost/tracker?page=1
>>
>> Best
>> Michael
>>
>>
>> On Jan 25, 2016, at 5:58 PM, Stephen Ficklin wrote:
>>
>>> Wonderful!  Yes, those warnings will unfortunately appear.  But, after you delete the view integrations (Step 17) they should be rebuilt and that message should go away.  I have made note of these warnings in the the upgrade instructions.
>>>
>>> Thanks for reaching out when you had issues.
>>>
>>> Stephen
>>>
>>> On 1/25/2016 6:20 AM, Michael Dondrup wrote:
>>>> Hi,
>>>>
>>>> thank you again. It worked!
>>>>
>>>> The dbupdate has been applied using the updated code.  There was only one repeated warning.
>>>>
>>>> in updating tripal_views
>>>>  [site https://...] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store relationship for studyprop_feature => feature when you should be using tripal_views_joins.
>>>>
>>>> I think we should take another snapshot here and start activating tripal core modules and see how that goes.
>>>>
>>>> Best
>>>> Michael
>>>>
>>>>
>>>> ----------------------------------------------------------------------------------------------------------------------------------------------
>>>> Below I will list the commands for our reference:
>>>>
>>>> # ALTER USER user SET search_path TO public; just to be shure
>>>>
>>>> ## applied taxonomy patch, but didn't start core update from scratch becasue we didn't have taxonomy errors
>>>>
>>>> ### starting from Snapshot step_12
>>>>
>>>> ## moved misplaced tables from chado to public in psql
>>>>
>>>> ALTER table chado.tripal_custom_tables set schema public;
>>>> ALTER table chado.tripal_gff_temp set schema public;
>>>> ALTER table chado.tripal_jobs set schema public;
>>>> ALTER table chado.tripal_mviews set schema public;
>>>> ALTER table chado.tripal_obo_temp set schema public;
>>>>
>>>>
>>>> ### Step 13.
>>>> drush pm-download views ctools
>>>> drush updatedb
>>>>
>>>> drush pm-enable ctools views views_ui
>>>>
>>>> ## all OK Snapshot taken step_13
>>>>
>>>> ### Step 14. modified to get latest beta
>>>>
>>>> cd sites/all/modules
>>>> git clone https://github.com/tripal/tripal.git -b 7.x-2.1-beta2
>>>> # warning: Remote branch 7.x-2.1-beta2 not found in upstream origin, using HEAD instead
>>>> cd tripal/
>>>> ## 7.x-2.1-beta2 is a tag
>>>> git checkout 7.x-2.1-beta2
>>>>
>>>> ### Step 15:
>>>> drush updatedb
>>>> ## all ok
>>>>
>>>> ### Step 16:
>>>>
>>>> drush pm-enable tripal_core
>>>> ## all ok
>>>> drush pm-enable tripal_views
>>>>
>>>> # repeated many times
>>>> # [site https://...] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store
>>>> # relationship for studyprop_feature => feature when you should be using tripal_views_joins.
>>>>
>>>> ### Step 17: Administration -> Tripal -> Views Integration -> click 'Delete All Integrations'
>>>> # Successfully deleted all views integration.
>>>> #Successfully rebuilt default Tripal Views Integrations
>>>>
>>>> ## Changed tripal_core.info to avoid update warnings
>>>>> version = 7.x-2.1-beta2
>>>>
>>>> On Jan 24, 2016, at 11:17 AM, Michael Dondrup wrote:
>>>>
>>>>> Hi Stephen,
>>>>> thank you so much for the quick response. I need to get our sysadmin involved to revert the database
>>>>> to the correct snapshot. I hope I will be ready testing before the afternoon on monday.
>>>>>
>>>>> Michael
>>>>>
>>>>> On Jan 23, 2016, at 9:11 PM, Stephen Ficklin wrote:
>>>>>
>>>>>> Hi Michael,
>>>>>>
>>>>>> I found one irritating bug that should have been fixed for the beta1 release. I've fixed it but Drupal.org won't let me redo the release to include the fix, so I had to issue a new beta2 release.  Also, I'm not sure the command I gave you below to download Tripal will work, and I can't test it to make sure until Drupal creates the files.  So use this instead:
>>>>>>
>>>>>> git clone [hidden email]:tripal/tripal.git -b 7.x-2.1-beta2
>>>>>>
>>>>>> Stephen
>>>>>>
>>>>>> On 1/23/2016 11:02 AM, Stephen Ficklin wrote:
>>>>>>> Hi Michael,
>>>>>>>
>>>>>>> The fixes are ready.  I have also adjusted the upgrade documentation to add a patch for a taxonomy bug that seems to occur for some people during upgrade.  I added a new step #10 to the upgrade documentation http://tripal.info/tutorials/v2.0/upgrade.    I also just released Tripal v2.1-beta1.  This is a precursor for our full Tripal v2.1 release (which will include support for Chado v1.3).
>>>>>>>
>>>>>>> So, in step #14 when it asks you download Tripal use this command instead
>>>>>>>
>>>>>>> drush pm-download tripal 7.x-2.1-beta1
>>>>>>>
>>>>>>> Drupal only rebuilds its releases at the end of the day so this beta release should be available tomorrow.
>>>>>>>
>>>>>>> I have tested an upgrade of Drupal 6 / Tripal v1 to Drupal 7 / Tripal v2 and it worked just fine without problems using this new beta1 version.
>>>>>>>
>>>>>>> Let me know if you have issues.
>>>>>>>
>>>>>>> Stephen
>>>>>>>
>>>>>>>
>>>>>>> On 1/22/2016 10:26 AM, Michael Dondrup wrote:
>>>>>>>> Hi Stephen,
>>>>>>>>
>>>>>>>> That would be great, we will just revert to the state directly after updating clean drupal core
>>>>>>>> next week.
>>>>>>>> Will php 5.3.3 and drush 6.7.0 be ok?
>>>>>>>>
>>>>>>>> Michael
>>>>>>>>
>>>>>>>>
>>>>>>>> On Jan 22, 2016, at 6:31 PM, Stephen Ficklin wrote:
>>>>>>>>
>>>>>>>>> Hi Michael,
>>>>>>>>>
>>>>>>>>> I believe I understand what the problem is.   I'm going to add a fix to Tripal v2.x (the development branch) and let you know when it's ready.  Can you use the development branch for testing your upgrade?  We're very close to releasing v2.1 so it should be stable enough to use.
>>>>>>>>>
>>>>>>>>> Stephen
>>>>>>>>>
>>>>>>>>> On 1/22/2016 2:39 AM, Michael Dondrup wrote:
>>>>>>>>>> Hi,
>>>>>>>>>> we are still getting the 'undefined function errors' for functions that are in reality defined in the code of tripal:
>>>>>>>>>> e.g. tripal_add_mview() or tripal_insert_obo(). These functions sometimes change erratically throughout the process.
>>>>>>>>>> We were suspecting the drush version as we were initially using drush 5.7, we have therefore tested with other
>>>>>>>>>> versions: 6.4 (as recommended in the documentation), 6.0, 6.7 (latest stable 6), 5.5.9. We also tried drush 7 branches, but
>>>>>>>>>> these don't recognize a drupal site.
>>>>>>>>>>
>>>>>>>>>> Drush install via composer, php version is PHP 5.3.3
>>>>>>>>>>
>>>>>>>>>> Each time we cleared the cache (drush cc all) and rebuilt the drush registry (drush rr). To no avail. As the process is a bit erratic
>>>>>>>>>> I interpret this as caused by the sequence of php file inclusions.
>>>>>>>>>>
>>>>>>>>>> We have certainly hit a wall here, and would appreciate any input as the migration is somewhat urgent to cmplete.
>>>>>>>>>>
>>>>>>>>>> Thank you in advance for your help.
>>>>>>>>>>
>>>>>>>>>> Michael
>>>>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>>> Full output below:
>>>>>>>>>>
>>>>>>>>>> $ drush updb
>>>>>>>>>> Tripal_core        7204  Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>>>>> Tripal_feature     7202  Adds the temporary tables used for loading GFF files.
>>>>>>>>>> Tripal_pub         7202  Updates path of tripal_pub OBO to be relative.
>>>>>>>>>> Tripal_stock       7201  Add materialized views
>>>>>>>>>> Tripal_contact     7202  Updates path of tripal_contact OBO to be relative.
>>>>>>>>>> Tripal_featuremap  7202  Fixes a typo when setting the default CV for the unittype_id field of the
>>>>>>>>>>                          featuremap table.
>>>>>>>>>> Do you wish to run all pending updates? (y/n): y
>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>>>>>>>>
>>>>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install, line 409
>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>> 'all' cache was cleared in self [success]
>>>>>>>>>> Finished performing updates. [ok]
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Jan 21, 2016, at 9:32 PM, Michael Dondrup wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Stephen,
>>>>>>>>>>>
>>>>>>>>>>> thank your for your response, I think we are getting closer to the core of the problem.
>>>>>>>>>>> Do you think this might cause also the 'call to undefined function' error?
>>>>>>>>>>>
>>>>>>>>>>> Michael
>>>>>>>>>>>
>>>>>>>>>>> On Jan 21, 2016, at 8:00 PM, Stephen Ficklin wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Michael,
>>>>>>>>>>>>
>>>>>>>>>>>> When you started your upgrade did you have the search_path set for the postrgreSQL user?
>>>>>>>>>>> Yes we had re-set the search path to public only.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> (Step 3 in upgrade procedue http://tripal.info/tutorials/v2.0/upgrade).  If so, then perhaps some of the tables that should be in the 'public' schema in your D6 site are in the 'chado' schema and they shouldn't be.
>>>>>>>>>>> I think this is the case: The following tripal* tables are in chado in our D6 system:
>>>>>>>>>>>
>>>>>>>>>>> licebase=> \dt chado.tripal*
>>>>>>>>>>>               List of relations
>>>>>>>>>>> Schema |         Name         | Type  |  Owner
>>>>>>>>>>> --------+----------------------+-------+----------
>>>>>>>>>>> chado  | tripal_custom_tables | table | lb_admin
>>>>>>>>>>> chado  | tripal_gff_temp      | table | lb_admin
>>>>>>>>>>> chado  | tripal_jobs          | table | lb_admin
>>>>>>>>>>> chado  | tripal_mviews        | table | lb_admin
>>>>>>>>>>> chado  | tripal_obo_temp      | table | lb_admin
>>>>>>>>>>> (5 rows)
>>>>>>>>>>>
>>>>>>>>>>> The following ones are in public
>>>>>>>>>>>
>>>>>>>>>>> licebase=> \dt public.tripal*
>>>>>>>>>>>                   List of relations
>>>>>>>>>>> Schema |             Name             | Type  |  Owner
>>>>>>>>>>> --------+------------------------------+-------+----------
>>>>>>>>>>> public | tripal_analysis              | table | lb_admin
>>>>>>>>>>> public | tripal_analysis_blast        | table | lb_admin
>>>>>>>>>>> public | tripal_bulk_loader           | table | lb_admin
>>>>>>>>>>> public | tripal_bulk_loader_constants | table | lb_admin
>>>>>>>>>>> public | tripal_bulk_loader_inserted  | table | lb_admin
>>>>>>>>>>> public | tripal_bulk_loader_template  | table | lb_admin
>>>>>>>>>>> public | tripal_cv_obo                | table | lb_admin
>>>>>>>>>>> public | tripal_feature_relagg        | table | lb_admin
>>>>>>>>>>> public | tripal_pub_import            | table | lb_admin
>>>>>>>>>>> public | tripal_views                 | table | lb_admin
>>>>>>>>>>> public | tripal_views_field           | table | lb_admin
>>>>>>>>>>> public | tripal_views_handlers        | table | lb_admin
>>>>>>>>>>> public | tripal_views_join            | table | lb_admin
>>>>>>>>>>> (13 rows)
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> I do remember a bug at one point in one of our development versions that caused this.  If this is the case then it makes sense that you would have problems during the upgrade.   Do you have a backup of your D6 site database where you can look to see if those tables are in the 'chado' schema?
>>>>>>>>>>> W are working on an identical copy, while the D6 Tripal1 system is still online and we have backups of each stage so we can start over. So I could just look it up in the
>>>>>>>>>>> production system.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> If so, moving them to the 'public' schema and then retrying the upgrade may help.  If you do see some of these tables in the 'chado' schema but you're unsure if there are more that should also be moved feel free to send the list of tables in your 'chado' schema and I can let you know.
>>>>>>>>>>> So should I first attempt move all those tripal* tables from chado to public? Funny enough this doesn't cause problems in the D6 system....
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> Stephen
>>>>>>>>>>>>
>>>>>>>>>>>> On 1/21/2016 1:15 AM, Michael Dondrup wrote:
>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>> we fixed the first problem somehow the tripal_custom_tables table was created in chado schema. I moved it
>>>>>>>>>>>>> ALTER TABLE tripal_custom_tables SET SCHEMA public;
>>>>>>>>>>>>>
>>>>>>>>>>>>> Leaving me with this error:
>>>>>>>>>>>>>
>>>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> This is weird because the function is certainly defined in tripal/tripal_cv/api/tripal_cv.api.inc:function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE)
>>>>>>>>>>>>>
>>>>>>>>>>>>> I have tried to drush cc all and even rebuilt the registry as described here: https://www.drupal.org/project/registry_rebuild
>>>>>>>>>>>>>
>>>>>>>>>>>>> But to no avail. Anybody else having this problem?
>>>>>>>>>>>>>
>>>>>>>>>>>>> I really appreciate your help.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Michael
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Jan 20, 2016, at 2:17 PM, Michael Dondrup wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> we are doing a test-run of the D6->7 migration of our site including a Tripal update, following http://tripal.info/tutorials/v2.0/upgrade
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> We are currently at step 14. Next, apply the Tripal updates: drush updatedb
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> All core updates, views and ctools have been performed without error and no pending db updates were scheduled prior to this step.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>>>>>>>>> does not exist
>>>>>>>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>>>>>>>      ^
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> [...]
>>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I guess we have a fix for the first one, however that yields different errors:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> The table tripal_mviews exists but in the schema chado. I tried to set the search_path back:
>>>>>>>>>>>>>> ALTER USER user SET search_path TO public, chado;
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> However this yields other errors:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Cannot add field tripal_custom_tables.mview_id: table doesn't exist. [error]
>>>>>>>>>>>>>> [...]
>>>>>>>>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install on line 449
>>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install, line 449
>>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I searched and found http://sourceforge.net/p/gmod/mailman/message/32762105/ but that doesn't seem to fit.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Best
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Michael Dondrup
>>>>>>>>>>>>>> Researcher
>>>>>>>>>>>>>> Sea Lice Research Centre
>>>>>>>>>>>>>> Department of Informatics
>>>>>>>>>>>>>> University of Bergen
>>>>>>>>>>>>>> Thormøhlensgate 55, N-5008 Bergen,
>>>>>>>>>>>>>> Norway
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Full output of drush updatedb first iteration:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> $ drush updatedb
>>>>>>>>>>>>>> The following updates are pending:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> tripal_core module :
>>>>>>>>>>>>>> 7200 -   Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table
>>>>>>>>>>>>>> 7201 -   Fixes missing language for nodes and URL aliases. This may take awhile...
>>>>>>>>>>>>>> 7202 -   Adds a tripal_token_formats table for custom page titles and URL paths
>>>>>>>>>>>>>> 7203 -   Adds a tripal_toc table for customizing the table of contents on each Tripal page.
>>>>>>>>>>>>>> 7204 -   Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> tripal_organism module :
>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> tripal_cv module :
>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> tripal_contact module :
>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>>>>>>>> 7202 -   Updates path of tripal_contact OBO to be relative.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> tripal_bulk_loader module :
>>>>>>>>>>>>>> 7200 -   Implements hook_update_N().   Update to 7.x-2.0  -Cast tripal_bulk_loader.template_id to int field
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> tripal_library module :
>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_library when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> tripal_stock module :
>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_stock when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>> 7201 -   Add materialized views
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> tripal_project module :
>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_project when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> tripal_analysis module :
>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> tripal_featuremap module :
>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_featuremap when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>>>>>>>> 7202 -   Fixes a typo when setting the default CV for the unittype_id field of the featuremap table.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> tripal_feature module :
>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_feature when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>> 7202 -   Adds the temporary tables used for loading GFF files.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> tripal_views module :
>>>>>>>>>>>>>> 7200 -   Tripal Views Update for 7.x-2.0    - Add relationship_only field to tripal_views_join    - Add relationship_handler field to tripal_views_join
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> tripal_pub module :
>>>>>>>>>>>>>> 7202 -   Updates path of tripal_pub OBO to be relative.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Performed update: tripal_feature_update_7200 [ok]
>>>>>>>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>>>>>>>>> does not exist
>>>>>>>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>>>>>>>      ^
>>>>>>>>>>>>>> Performed update: tripal_feature_update_7201 [ok]
>>>>>>>>>>>>>> Performed update: tripal_featuremap_update_7200 [ok]
>>>>>>>>>>>>>> Performed update: tripal_featuremap_update_7201 [ok]
>>>>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Fatal error: Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>>> Finished performing updates. [ok]
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>>>>>>> Full output after setting search_path to public, chado
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>> [hidden email]
>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Stephen Ficklin-2
Hmmm.....

In your tripal/tripal_core/api directory there should be this file:

tripal_core.chado_nodes.title_and_path.api.inc

Note:  it should have 'api' in the name.  Is it there for you?

Stephen


On 1/25/2016 9:51 PM, Michael Dondrup wrote:

> Hi,
>
> I pulled the latest 7.x-2.1-beta2 but the error is still the same.
>
> Michael
>
> On Jan 26, 2016, at 2:12 AM, Stephen Ficklin wrote:
>
>> Hi Michael,
>>
>> No need to apologize.   This was my mistake. I made a typo in the fix I made to get you passed the upgrade problems.  I fixed it, tested on my end and seems to be fine.  Please pull the most recent version of the development code from the git repository and you should have the fix.
>>
>> Please let me know if you have additional issues.
>>
>> Stephen
>>
>> On 1/25/2016 1:32 PM, Michael Dondrup wrote:
>>> Here we go, sorry to bother again.
>>> After enabling tripal_feature and most other tripal modules, when trying to access a feature I get:
>>>
>>> PHP Fatal error:  Call to undefined function chado_get_node_title() in /home/licebase/d7/sites/all/modules/tripal/tripal_feature/includes/tripal_feature.chado_node.inc on line 738, referer: https://localhost/tracker?page=1
>>>
>>> Best
>>> Michael
>>>
>>>
>>> On Jan 25, 2016, at 5:58 PM, Stephen Ficklin wrote:
>>>
>>>> Wonderful!  Yes, those warnings will unfortunately appear.  But, after you delete the view integrations (Step 17) they should be rebuilt and that message should go away.  I have made note of these warnings in the the upgrade instructions.
>>>>
>>>> Thanks for reaching out when you had issues.
>>>>
>>>> Stephen
>>>>
>>>> On 1/25/2016 6:20 AM, Michael Dondrup wrote:
>>>>> Hi,
>>>>>
>>>>> thank you again. It worked!
>>>>>
>>>>> The dbupdate has been applied using the updated code.  There was only one repeated warning.
>>>>>
>>>>> in updating tripal_views
>>>>>   [site https://...] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store relationship for studyprop_feature => feature when you should be using tripal_views_joins.
>>>>>
>>>>> I think we should take another snapshot here and start activating tripal core modules and see how that goes.
>>>>>
>>>>> Best
>>>>> Michael
>>>>>
>>>>>
>>>>> ----------------------------------------------------------------------------------------------------------------------------------------------
>>>>> Below I will list the commands for our reference:
>>>>>
>>>>> # ALTER USER user SET search_path TO public; just to be shure
>>>>>
>>>>> ## applied taxonomy patch, but didn't start core update from scratch becasue we didn't have taxonomy errors
>>>>>
>>>>> ### starting from Snapshot step_12
>>>>>
>>>>> ## moved misplaced tables from chado to public in psql
>>>>>
>>>>> ALTER table chado.tripal_custom_tables set schema public;
>>>>> ALTER table chado.tripal_gff_temp set schema public;
>>>>> ALTER table chado.tripal_jobs set schema public;
>>>>> ALTER table chado.tripal_mviews set schema public;
>>>>> ALTER table chado.tripal_obo_temp set schema public;
>>>>>
>>>>>
>>>>> ### Step 13.
>>>>> drush pm-download views ctools
>>>>> drush updatedb
>>>>>
>>>>> drush pm-enable ctools views views_ui
>>>>>
>>>>> ## all OK Snapshot taken step_13
>>>>>
>>>>> ### Step 14. modified to get latest beta
>>>>>
>>>>> cd sites/all/modules
>>>>> git clone https://github.com/tripal/tripal.git -b 7.x-2.1-beta2
>>>>> # warning: Remote branch 7.x-2.1-beta2 not found in upstream origin, using HEAD instead
>>>>> cd tripal/
>>>>> ## 7.x-2.1-beta2 is a tag
>>>>> git checkout 7.x-2.1-beta2
>>>>>
>>>>> ### Step 15:
>>>>> drush updatedb
>>>>> ## all ok
>>>>>
>>>>> ### Step 16:
>>>>>
>>>>> drush pm-enable tripal_core
>>>>> ## all ok
>>>>> drush pm-enable tripal_views
>>>>>
>>>>> # repeated many times
>>>>> # [site https://...] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store
>>>>> # relationship for studyprop_feature => feature when you should be using tripal_views_joins.
>>>>>
>>>>> ### Step 17: Administration -> Tripal -> Views Integration -> click 'Delete All Integrations'
>>>>> # Successfully deleted all views integration.
>>>>> #Successfully rebuilt default Tripal Views Integrations
>>>>>
>>>>> ## Changed tripal_core.info to avoid update warnings
>>>>>> version = 7.x-2.1-beta2
>>>>> On Jan 24, 2016, at 11:17 AM, Michael Dondrup wrote:
>>>>>
>>>>>> Hi Stephen,
>>>>>> thank you so much for the quick response. I need to get our sysadmin involved to revert the database
>>>>>> to the correct snapshot. I hope I will be ready testing before the afternoon on monday.
>>>>>>
>>>>>> Michael
>>>>>>
>>>>>> On Jan 23, 2016, at 9:11 PM, Stephen Ficklin wrote:
>>>>>>
>>>>>>> Hi Michael,
>>>>>>>
>>>>>>> I found one irritating bug that should have been fixed for the beta1 release. I've fixed it but Drupal.org won't let me redo the release to include the fix, so I had to issue a new beta2 release.  Also, I'm not sure the command I gave you below to download Tripal will work, and I can't test it to make sure until Drupal creates the files.  So use this instead:
>>>>>>>
>>>>>>> git clone [hidden email]:tripal/tripal.git -b 7.x-2.1-beta2
>>>>>>>
>>>>>>> Stephen
>>>>>>>
>>>>>>> On 1/23/2016 11:02 AM, Stephen Ficklin wrote:
>>>>>>>> Hi Michael,
>>>>>>>>
>>>>>>>> The fixes are ready.  I have also adjusted the upgrade documentation to add a patch for a taxonomy bug that seems to occur for some people during upgrade.  I added a new step #10 to the upgrade documentation http://tripal.info/tutorials/v2.0/upgrade.    I also just released Tripal v2.1-beta1.  This is a precursor for our full Tripal v2.1 release (which will include support for Chado v1.3).
>>>>>>>>
>>>>>>>> So, in step #14 when it asks you download Tripal use this command instead
>>>>>>>>
>>>>>>>> drush pm-download tripal 7.x-2.1-beta1
>>>>>>>>
>>>>>>>> Drupal only rebuilds its releases at the end of the day so this beta release should be available tomorrow.
>>>>>>>>
>>>>>>>> I have tested an upgrade of Drupal 6 / Tripal v1 to Drupal 7 / Tripal v2 and it worked just fine without problems using this new beta1 version.
>>>>>>>>
>>>>>>>> Let me know if you have issues.
>>>>>>>>
>>>>>>>> Stephen
>>>>>>>>
>>>>>>>>
>>>>>>>> On 1/22/2016 10:26 AM, Michael Dondrup wrote:
>>>>>>>>> Hi Stephen,
>>>>>>>>>
>>>>>>>>> That would be great, we will just revert to the state directly after updating clean drupal core
>>>>>>>>> next week.
>>>>>>>>> Will php 5.3.3 and drush 6.7.0 be ok?
>>>>>>>>>
>>>>>>>>> Michael
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Jan 22, 2016, at 6:31 PM, Stephen Ficklin wrote:
>>>>>>>>>
>>>>>>>>>> Hi Michael,
>>>>>>>>>>
>>>>>>>>>> I believe I understand what the problem is.   I'm going to add a fix to Tripal v2.x (the development branch) and let you know when it's ready.  Can you use the development branch for testing your upgrade?  We're very close to releasing v2.1 so it should be stable enough to use.
>>>>>>>>>>
>>>>>>>>>> Stephen
>>>>>>>>>>
>>>>>>>>>> On 1/22/2016 2:39 AM, Michael Dondrup wrote:
>>>>>>>>>>> Hi,
>>>>>>>>>>> we are still getting the 'undefined function errors' for functions that are in reality defined in the code of tripal:
>>>>>>>>>>> e.g. tripal_add_mview() or tripal_insert_obo(). These functions sometimes change erratically throughout the process.
>>>>>>>>>>> We were suspecting the drush version as we were initially using drush 5.7, we have therefore tested with other
>>>>>>>>>>> versions: 6.4 (as recommended in the documentation), 6.0, 6.7 (latest stable 6), 5.5.9. We also tried drush 7 branches, but
>>>>>>>>>>> these don't recognize a drupal site.
>>>>>>>>>>>
>>>>>>>>>>> Drush install via composer, php version is PHP 5.3.3
>>>>>>>>>>>
>>>>>>>>>>> Each time we cleared the cache (drush cc all) and rebuilt the drush registry (drush rr). To no avail. As the process is a bit erratic
>>>>>>>>>>> I interpret this as caused by the sequence of php file inclusions.
>>>>>>>>>>>
>>>>>>>>>>> We have certainly hit a wall here, and would appreciate any input as the migration is somewhat urgent to cmplete.
>>>>>>>>>>>
>>>>>>>>>>> Thank you in advance for your help.
>>>>>>>>>>>
>>>>>>>>>>> Michael
>>>>>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>>>> Full output below:
>>>>>>>>>>>
>>>>>>>>>>> $ drush updb
>>>>>>>>>>> Tripal_core        7204  Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>>>>>> Tripal_feature     7202  Adds the temporary tables used for loading GFF files.
>>>>>>>>>>> Tripal_pub         7202  Updates path of tripal_pub OBO to be relative.
>>>>>>>>>>> Tripal_stock       7201  Add materialized views
>>>>>>>>>>> Tripal_contact     7202  Updates path of tripal_contact OBO to be relative.
>>>>>>>>>>> Tripal_featuremap  7202  Fixes a typo when setting the default CV for the unittype_id field of the
>>>>>>>>>>>                           featuremap table.
>>>>>>>>>>> Do you wish to run all pending updates? (y/n): y
>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>>>>>>>>>
>>>>>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>>>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install, line 409
>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>> 'all' cache was cleared in self [success]
>>>>>>>>>>> Finished performing updates. [ok]
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Jan 21, 2016, at 9:32 PM, Michael Dondrup wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Stephen,
>>>>>>>>>>>>
>>>>>>>>>>>> thank your for your response, I think we are getting closer to the core of the problem.
>>>>>>>>>>>> Do you think this might cause also the 'call to undefined function' error?
>>>>>>>>>>>>
>>>>>>>>>>>> Michael
>>>>>>>>>>>>
>>>>>>>>>>>> On Jan 21, 2016, at 8:00 PM, Stephen Ficklin wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Michael,
>>>>>>>>>>>>>
>>>>>>>>>>>>> When you started your upgrade did you have the search_path set for the postrgreSQL user?
>>>>>>>>>>>> Yes we had re-set the search path to public only.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> (Step 3 in upgrade procedue http://tripal.info/tutorials/v2.0/upgrade).  If so, then perhaps some of the tables that should be in the 'public' schema in your D6 site are in the 'chado' schema and they shouldn't be.
>>>>>>>>>>>> I think this is the case: The following tripal* tables are in chado in our D6 system:
>>>>>>>>>>>>
>>>>>>>>>>>> licebase=> \dt chado.tripal*
>>>>>>>>>>>>                List of relations
>>>>>>>>>>>> Schema |         Name         | Type  |  Owner
>>>>>>>>>>>> --------+----------------------+-------+----------
>>>>>>>>>>>> chado  | tripal_custom_tables | table | lb_admin
>>>>>>>>>>>> chado  | tripal_gff_temp      | table | lb_admin
>>>>>>>>>>>> chado  | tripal_jobs          | table | lb_admin
>>>>>>>>>>>> chado  | tripal_mviews        | table | lb_admin
>>>>>>>>>>>> chado  | tripal_obo_temp      | table | lb_admin
>>>>>>>>>>>> (5 rows)
>>>>>>>>>>>>
>>>>>>>>>>>> The following ones are in public
>>>>>>>>>>>>
>>>>>>>>>>>> licebase=> \dt public.tripal*
>>>>>>>>>>>>                    List of relations
>>>>>>>>>>>> Schema |             Name             | Type  |  Owner
>>>>>>>>>>>> --------+------------------------------+-------+----------
>>>>>>>>>>>> public | tripal_analysis              | table | lb_admin
>>>>>>>>>>>> public | tripal_analysis_blast        | table | lb_admin
>>>>>>>>>>>> public | tripal_bulk_loader           | table | lb_admin
>>>>>>>>>>>> public | tripal_bulk_loader_constants | table | lb_admin
>>>>>>>>>>>> public | tripal_bulk_loader_inserted  | table | lb_admin
>>>>>>>>>>>> public | tripal_bulk_loader_template  | table | lb_admin
>>>>>>>>>>>> public | tripal_cv_obo                | table | lb_admin
>>>>>>>>>>>> public | tripal_feature_relagg        | table | lb_admin
>>>>>>>>>>>> public | tripal_pub_import            | table | lb_admin
>>>>>>>>>>>> public | tripal_views                 | table | lb_admin
>>>>>>>>>>>> public | tripal_views_field           | table | lb_admin
>>>>>>>>>>>> public | tripal_views_handlers        | table | lb_admin
>>>>>>>>>>>> public | tripal_views_join            | table | lb_admin
>>>>>>>>>>>> (13 rows)
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> I do remember a bug at one point in one of our development versions that caused this.  If this is the case then it makes sense that you would have problems during the upgrade.   Do you have a backup of your D6 site database where you can look to see if those tables are in the 'chado' schema?
>>>>>>>>>>>> W are working on an identical copy, while the D6 Tripal1 system is still online and we have backups of each stage so we can start over. So I could just look it up in the
>>>>>>>>>>>> production system.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> If so, moving them to the 'public' schema and then retrying the upgrade may help.  If you do see some of these tables in the 'chado' schema but you're unsure if there are more that should also be moved feel free to send the list of tables in your 'chado' schema and I can let you know.
>>>>>>>>>>>> So should I first attempt move all those tripal* tables from chado to public? Funny enough this doesn't cause problems in the D6 system....
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> Stephen
>>>>>>>>>>>>>
>>>>>>>>>>>>> On 1/21/2016 1:15 AM, Michael Dondrup wrote:
>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>> we fixed the first problem somehow the tripal_custom_tables table was created in chado schema. I moved it
>>>>>>>>>>>>>> ALTER TABLE tripal_custom_tables SET SCHEMA public;
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Leaving me with this error:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> This is weird because the function is certainly defined in tripal/tripal_cv/api/tripal_cv.api.inc:function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE)
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I have tried to drush cc all and even rebuilt the registry as described here: https://www.drupal.org/project/registry_rebuild
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> But to no avail. Anybody else having this problem?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I really appreciate your help.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Michael
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Jan 20, 2016, at 2:17 PM, Michael Dondrup wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> we are doing a test-run of the D6->7 migration of our site including a Tripal update, following http://tripal.info/tutorials/v2.0/upgrade
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> We are currently at step 14. Next, apply the Tripal updates: drush updatedb
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> All core updates, views and ctools have been performed without error and no pending db updates were scheduled prior to this step.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>>>>>>>>>> does not exist
>>>>>>>>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>>>>>>>>       ^
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> [...]
>>>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I guess we have a fix for the first one, however that yields different errors:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> The table tripal_mviews exists but in the schema chado. I tried to set the search_path back:
>>>>>>>>>>>>>>> ALTER USER user SET search_path TO public, chado;
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> However this yields other errors:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Cannot add field tripal_custom_tables.mview_id: table doesn't exist. [error]
>>>>>>>>>>>>>>> [...]
>>>>>>>>>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install on line 449
>>>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install, line 449
>>>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I searched and found http://sourceforge.net/p/gmod/mailman/message/32762105/ but that doesn't seem to fit.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Best
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Michael Dondrup
>>>>>>>>>>>>>>> Researcher
>>>>>>>>>>>>>>> Sea Lice Research Centre
>>>>>>>>>>>>>>> Department of Informatics
>>>>>>>>>>>>>>> University of Bergen
>>>>>>>>>>>>>>> Thormøhlensgate 55, N-5008 Bergen,
>>>>>>>>>>>>>>> Norway
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Full output of drush updatedb first iteration:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> $ drush updatedb
>>>>>>>>>>>>>>> The following updates are pending:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> tripal_core module :
>>>>>>>>>>>>>>> 7200 -   Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table
>>>>>>>>>>>>>>> 7201 -   Fixes missing language for nodes and URL aliases. This may take awhile...
>>>>>>>>>>>>>>> 7202 -   Adds a tripal_token_formats table for custom page titles and URL paths
>>>>>>>>>>>>>>> 7203 -   Adds a tripal_toc table for customizing the table of contents on each Tripal page.
>>>>>>>>>>>>>>> 7204 -   Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> tripal_organism module :
>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> tripal_cv module :
>>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> tripal_contact module :
>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>>>>>>>>> 7202 -   Updates path of tripal_contact OBO to be relative.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> tripal_bulk_loader module :
>>>>>>>>>>>>>>> 7200 -   Implements hook_update_N().   Update to 7.x-2.0  -Cast tripal_bulk_loader.template_id to int field
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> tripal_library module :
>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_library when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> tripal_stock module :
>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_stock when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>> 7201 -   Add materialized views
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> tripal_project module :
>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_project when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> tripal_analysis module :
>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> tripal_featuremap module :
>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_featuremap when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>>>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>>>>>>>>> 7202 -   Fixes a typo when setting the default CV for the unittype_id field of the featuremap table.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> tripal_feature module :
>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_feature when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>> 7202 -   Adds the temporary tables used for loading GFF files.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> tripal_views module :
>>>>>>>>>>>>>>> 7200 -   Tripal Views Update for 7.x-2.0    - Add relationship_only field to tripal_views_join    - Add relationship_handler field to tripal_views_join
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> tripal_pub module :
>>>>>>>>>>>>>>> 7202 -   Updates path of tripal_pub OBO to be relative.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Performed update: tripal_feature_update_7200 [ok]
>>>>>>>>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>>>>>>>>>> does not exist
>>>>>>>>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>>>>>>>>       ^
>>>>>>>>>>>>>>> Performed update: tripal_feature_update_7201 [ok]
>>>>>>>>>>>>>>> Performed update: tripal_featuremap_update_7200 [ok]
>>>>>>>>>>>>>>> Performed update: tripal_featuremap_update_7201 [ok]
>>>>>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Fatal error: Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>>>> Finished performing updates. [ok]
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>>>>>>>> Full output after setting search_path to public, chado
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Michael Dondrup-3
Hi Stephen,
I don't seem to have have this file,
these are all the tripal_core api files I have.


$  find . -iname "tripal_core*api*"
./tripal_core/api/tripal_core.chado_nodes.relationships.api.inc
./tripal_core/api/tripal_core.chado_variables.api.inc
./tripal_core/api/tripal_core.tripal_variables.api.inc
./tripal_core/api/tripal_core.chado_query.api.inc
./tripal_core/api/tripal_core.tripal.api.inc
./tripal_core/api/tripal_core.files.api.inc
./tripal_core/api/tripal_core.custom_tables.api.inc
./tripal_core/api/tripal_core.schema_v1.2.api.inc
./tripal_core/api/tripal_core.d3js.api.inc
./tripal_core/api/tripal_core.chado_nodes.api.inc
./tripal_core/api/tripal_core.chado_general.api.inc
./tripal_core/api/tripal_core.chado_schema.api.inc
./tripal_core/api/tripal_core.chado_nodes.dbxrefs.api.inc
./tripal_core/api/tripal_core.chado_nodes.properties.api.inc
./tripal_core/api/tripal_core.schema_v1.11.api.inc
./tripal_core/api/tripal_core.mviews.api.inc
./tripal_core/api/tripal_core.jobs.api.inc


Michael

On Jan 26, 2016, at 7:02 AM, Stephen Ficklin wrote:

> Hmmm.....
>
> In your tripal/tripal_core/api directory there should be this file:
>
> tripal_core.chado_nodes.title_and_path.api.inc
>
> Note:  it should have 'api' in the name.  Is it there for you?
>
> Stephen
>
>
> On 1/25/2016 9:51 PM, Michael Dondrup wrote:
>> Hi,
>>
>> I pulled the latest 7.x-2.1-beta2 but the error is still the same.
>>
>> Michael
>>
>> On Jan 26, 2016, at 2:12 AM, Stephen Ficklin wrote:
>>
>>> Hi Michael,
>>>
>>> No need to apologize.   This was my mistake. I made a typo in the fix I made to get you passed the upgrade problems.  I fixed it, tested on my end and seems to be fine.  Please pull the most recent version of the development code from the git repository and you should have the fix.
>>>
>>> Please let me know if you have additional issues.
>>>
>>> Stephen
>>>
>>> On 1/25/2016 1:32 PM, Michael Dondrup wrote:
>>>> Here we go, sorry to bother again.
>>>> After enabling tripal_feature and most other tripal modules, when trying to access a feature I get:
>>>>
>>>> PHP Fatal error:  Call to undefined function chado_get_node_title() in /home/licebase/d7/sites/all/modules/tripal/tripal_feature/includes/tripal_feature.chado_node.inc on line 738, referer: https://localhost/tracker?page=1
>>>>
>>>> Best
>>>> Michael
>>>>
>>>>
>>>> On Jan 25, 2016, at 5:58 PM, Stephen Ficklin wrote:
>>>>
>>>>> Wonderful!  Yes, those warnings will unfortunately appear.  But, after you delete the view integrations (Step 17) they should be rebuilt and that message should go away.  I have made note of these warnings in the the upgrade instructions.
>>>>>
>>>>> Thanks for reaching out when you had issues.
>>>>>
>>>>> Stephen
>>>>>
>>>>> On 1/25/2016 6:20 AM, Michael Dondrup wrote:
>>>>>> Hi,
>>>>>>
>>>>>> thank you again. It worked!
>>>>>>
>>>>>> The dbupdate has been applied using the updated code.  There was only one repeated warning.
>>>>>>
>>>>>> in updating tripal_views
>>>>>>  [site https://...] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store relationship for studyprop_feature => feature when you should be using tripal_views_joins.
>>>>>>
>>>>>> I think we should take another snapshot here and start activating tripal core modules and see how that goes.
>>>>>>
>>>>>> Best
>>>>>> Michael
>>>>>>
>>>>>>
>>>>>> ----------------------------------------------------------------------------------------------------------------------------------------------
>>>>>> Below I will list the commands for our reference:
>>>>>>
>>>>>> # ALTER USER user SET search_path TO public; just to be shure
>>>>>>
>>>>>> ## applied taxonomy patch, but didn't start core update from scratch becasue we didn't have taxonomy errors
>>>>>>
>>>>>> ### starting from Snapshot step_12
>>>>>>
>>>>>> ## moved misplaced tables from chado to public in psql
>>>>>>
>>>>>> ALTER table chado.tripal_custom_tables set schema public;
>>>>>> ALTER table chado.tripal_gff_temp set schema public;
>>>>>> ALTER table chado.tripal_jobs set schema public;
>>>>>> ALTER table chado.tripal_mviews set schema public;
>>>>>> ALTER table chado.tripal_obo_temp set schema public;
>>>>>>
>>>>>>
>>>>>> ### Step 13.
>>>>>> drush pm-download views ctools
>>>>>> drush updatedb
>>>>>>
>>>>>> drush pm-enable ctools views views_ui
>>>>>>
>>>>>> ## all OK Snapshot taken step_13
>>>>>>
>>>>>> ### Step 14. modified to get latest beta
>>>>>>
>>>>>> cd sites/all/modules
>>>>>> git clone https://github.com/tripal/tripal.git -b 7.x-2.1-beta2
>>>>>> # warning: Remote branch 7.x-2.1-beta2 not found in upstream origin, using HEAD instead
>>>>>> cd tripal/
>>>>>> ## 7.x-2.1-beta2 is a tag
>>>>>> git checkout 7.x-2.1-beta2
>>>>>>
>>>>>> ### Step 15:
>>>>>> drush updatedb
>>>>>> ## all ok
>>>>>>
>>>>>> ### Step 16:
>>>>>>
>>>>>> drush pm-enable tripal_core
>>>>>> ## all ok
>>>>>> drush pm-enable tripal_views
>>>>>>
>>>>>> # repeated many times
>>>>>> # [site https://...] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store
>>>>>> # relationship for studyprop_feature => feature when you should be using tripal_views_joins.
>>>>>>
>>>>>> ### Step 17: Administration -> Tripal -> Views Integration -> click 'Delete All Integrations'
>>>>>> # Successfully deleted all views integration.
>>>>>> #Successfully rebuilt default Tripal Views Integrations
>>>>>>
>>>>>> ## Changed tripal_core.info to avoid update warnings
>>>>>>> version = 7.x-2.1-beta2
>>>>>> On Jan 24, 2016, at 11:17 AM, Michael Dondrup wrote:
>>>>>>
>>>>>>> Hi Stephen,
>>>>>>> thank you so much for the quick response. I need to get our sysadmin involved to revert the database
>>>>>>> to the correct snapshot. I hope I will be ready testing before the afternoon on monday.
>>>>>>>
>>>>>>> Michael
>>>>>>>
>>>>>>> On Jan 23, 2016, at 9:11 PM, Stephen Ficklin wrote:
>>>>>>>
>>>>>>>> Hi Michael,
>>>>>>>>
>>>>>>>> I found one irritating bug that should have been fixed for the beta1 release. I've fixed it but Drupal.org won't let me redo the release to include the fix, so I had to issue a new beta2 release.  Also, I'm not sure the command I gave you below to download Tripal will work, and I can't test it to make sure until Drupal creates the files.  So use this instead:
>>>>>>>>
>>>>>>>> git clone [hidden email]:tripal/tripal.git -b 7.x-2.1-beta2
>>>>>>>>
>>>>>>>> Stephen
>>>>>>>>
>>>>>>>> On 1/23/2016 11:02 AM, Stephen Ficklin wrote:
>>>>>>>>> Hi Michael,
>>>>>>>>>
>>>>>>>>> The fixes are ready.  I have also adjusted the upgrade documentation to add a patch for a taxonomy bug that seems to occur for some people during upgrade.  I added a new step #10 to the upgrade documentation http://tripal.info/tutorials/v2.0/upgrade.    I also just released Tripal v2.1-beta1.  This is a precursor for our full Tripal v2.1 release (which will include support for Chado v1.3).
>>>>>>>>>
>>>>>>>>> So, in step #14 when it asks you download Tripal use this command instead
>>>>>>>>>
>>>>>>>>> drush pm-download tripal 7.x-2.1-beta1
>>>>>>>>>
>>>>>>>>> Drupal only rebuilds its releases at the end of the day so this beta release should be available tomorrow.
>>>>>>>>>
>>>>>>>>> I have tested an upgrade of Drupal 6 / Tripal v1 to Drupal 7 / Tripal v2 and it worked just fine without problems using this new beta1 version.
>>>>>>>>>
>>>>>>>>> Let me know if you have issues.
>>>>>>>>>
>>>>>>>>> Stephen
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 1/22/2016 10:26 AM, Michael Dondrup wrote:
>>>>>>>>>> Hi Stephen,
>>>>>>>>>>
>>>>>>>>>> That would be great, we will just revert to the state directly after updating clean drupal core
>>>>>>>>>> next week.
>>>>>>>>>> Will php 5.3.3 and drush 6.7.0 be ok?
>>>>>>>>>>
>>>>>>>>>> Michael
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Jan 22, 2016, at 6:31 PM, Stephen Ficklin wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Michael,
>>>>>>>>>>>
>>>>>>>>>>> I believe I understand what the problem is.   I'm going to add a fix to Tripal v2.x (the development branch) and let you know when it's ready.  Can you use the development branch for testing your upgrade?  We're very close to releasing v2.1 so it should be stable enough to use.
>>>>>>>>>>>
>>>>>>>>>>> Stephen
>>>>>>>>>>>
>>>>>>>>>>> On 1/22/2016 2:39 AM, Michael Dondrup wrote:
>>>>>>>>>>>> Hi,
>>>>>>>>>>>> we are still getting the 'undefined function errors' for functions that are in reality defined in the code of tripal:
>>>>>>>>>>>> e.g. tripal_add_mview() or tripal_insert_obo(). These functions sometimes change erratically throughout the process.
>>>>>>>>>>>> We were suspecting the drush version as we were initially using drush 5.7, we have therefore tested with other
>>>>>>>>>>>> versions: 6.4 (as recommended in the documentation), 6.0, 6.7 (latest stable 6), 5.5.9. We also tried drush 7 branches, but
>>>>>>>>>>>> these don't recognize a drupal site.
>>>>>>>>>>>>
>>>>>>>>>>>> Drush install via composer, php version is PHP 5.3.3
>>>>>>>>>>>>
>>>>>>>>>>>> Each time we cleared the cache (drush cc all) and rebuilt the drush registry (drush rr). To no avail. As the process is a bit erratic
>>>>>>>>>>>> I interpret this as caused by the sequence of php file inclusions.
>>>>>>>>>>>>
>>>>>>>>>>>> We have certainly hit a wall here, and would appreciate any input as the migration is somewhat urgent to cmplete.
>>>>>>>>>>>>
>>>>>>>>>>>> Thank you in advance for your help.
>>>>>>>>>>>>
>>>>>>>>>>>> Michael
>>>>>>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>>>>> Full output below:
>>>>>>>>>>>>
>>>>>>>>>>>> $ drush updb
>>>>>>>>>>>> Tripal_core        7204  Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>>>>>>> Tripal_feature     7202  Adds the temporary tables used for loading GFF files.
>>>>>>>>>>>> Tripal_pub         7202  Updates path of tripal_pub OBO to be relative.
>>>>>>>>>>>> Tripal_stock       7201  Add materialized views
>>>>>>>>>>>> Tripal_contact     7202  Updates path of tripal_contact OBO to be relative.
>>>>>>>>>>>> Tripal_featuremap  7202  Fixes a typo when setting the default CV for the unittype_id field of the
>>>>>>>>>>>>                          featuremap table.
>>>>>>>>>>>> Do you wish to run all pending updates? (y/n): y
>>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>>>>>>>>>>
>>>>>>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>>>>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install, line 409
>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>> 'all' cache was cleared in self [success]
>>>>>>>>>>>> Finished performing updates. [ok]
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Jan 21, 2016, at 9:32 PM, Michael Dondrup wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Stephen,
>>>>>>>>>>>>>
>>>>>>>>>>>>> thank your for your response, I think we are getting closer to the core of the problem.
>>>>>>>>>>>>> Do you think this might cause also the 'call to undefined function' error?
>>>>>>>>>>>>>
>>>>>>>>>>>>> Michael
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Jan 21, 2016, at 8:00 PM, Stephen Ficklin wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Michael,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> When you started your upgrade did you have the search_path set for the postrgreSQL user?
>>>>>>>>>>>>> Yes we had re-set the search path to public only.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>> (Step 3 in upgrade procedue http://tripal.info/tutorials/v2.0/upgrade).  If so, then perhaps some of the tables that should be in the 'public' schema in your D6 site are in the 'chado' schema and they shouldn't be.
>>>>>>>>>>>>> I think this is the case: The following tripal* tables are in chado in our D6 system:
>>>>>>>>>>>>>
>>>>>>>>>>>>> licebase=> \dt chado.tripal*
>>>>>>>>>>>>>               List of relations
>>>>>>>>>>>>> Schema |         Name         | Type  |  Owner
>>>>>>>>>>>>> --------+----------------------+-------+----------
>>>>>>>>>>>>> chado  | tripal_custom_tables | table | lb_admin
>>>>>>>>>>>>> chado  | tripal_gff_temp      | table | lb_admin
>>>>>>>>>>>>> chado  | tripal_jobs          | table | lb_admin
>>>>>>>>>>>>> chado  | tripal_mviews        | table | lb_admin
>>>>>>>>>>>>> chado  | tripal_obo_temp      | table | lb_admin
>>>>>>>>>>>>> (5 rows)
>>>>>>>>>>>>>
>>>>>>>>>>>>> The following ones are in public
>>>>>>>>>>>>>
>>>>>>>>>>>>> licebase=> \dt public.tripal*
>>>>>>>>>>>>>                   List of relations
>>>>>>>>>>>>> Schema |             Name             | Type  |  Owner
>>>>>>>>>>>>> --------+------------------------------+-------+----------
>>>>>>>>>>>>> public | tripal_analysis              | table | lb_admin
>>>>>>>>>>>>> public | tripal_analysis_blast        | table | lb_admin
>>>>>>>>>>>>> public | tripal_bulk_loader           | table | lb_admin
>>>>>>>>>>>>> public | tripal_bulk_loader_constants | table | lb_admin
>>>>>>>>>>>>> public | tripal_bulk_loader_inserted  | table | lb_admin
>>>>>>>>>>>>> public | tripal_bulk_loader_template  | table | lb_admin
>>>>>>>>>>>>> public | tripal_cv_obo                | table | lb_admin
>>>>>>>>>>>>> public | tripal_feature_relagg        | table | lb_admin
>>>>>>>>>>>>> public | tripal_pub_import            | table | lb_admin
>>>>>>>>>>>>> public | tripal_views                 | table | lb_admin
>>>>>>>>>>>>> public | tripal_views_field           | table | lb_admin
>>>>>>>>>>>>> public | tripal_views_handlers        | table | lb_admin
>>>>>>>>>>>>> public | tripal_views_join            | table | lb_admin
>>>>>>>>>>>>> (13 rows)
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>> I do remember a bug at one point in one of our development versions that caused this.  If this is the case then it makes sense that you would have problems during the upgrade.   Do you have a backup of your D6 site database where you can look to see if those tables are in the 'chado' schema?
>>>>>>>>>>>>> W are working on an identical copy, while the D6 Tripal1 system is still online and we have backups of each stage so we can start over. So I could just look it up in the
>>>>>>>>>>>>> production system.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>> If so, moving them to the 'public' schema and then retrying the upgrade may help.  If you do see some of these tables in the 'chado' schema but you're unsure if there are more that should also be moved feel free to send the list of tables in your 'chado' schema and I can let you know.
>>>>>>>>>>>>> So should I first attempt move all those tripal* tables from chado to public? Funny enough this doesn't cause problems in the D6 system....
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Stephen
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On 1/21/2016 1:15 AM, Michael Dondrup wrote:
>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>> we fixed the first problem somehow the tripal_custom_tables table was created in chado schema. I moved it
>>>>>>>>>>>>>>> ALTER TABLE tripal_custom_tables SET SCHEMA public;
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Leaving me with this error:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> This is weird because the function is certainly defined in tripal/tripal_cv/api/tripal_cv.api.inc:function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE)
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I have tried to drush cc all and even rebuilt the registry as described here: https://www.drupal.org/project/registry_rebuild
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> But to no avail. Anybody else having this problem?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I really appreciate your help.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Michael
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Jan 20, 2016, at 2:17 PM, Michael Dondrup wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> we are doing a test-run of the D6->7 migration of our site including a Tripal update, following http://tripal.info/tutorials/v2.0/upgrade
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> We are currently at step 14. Next, apply the Tripal updates: drush updatedb
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> All core updates, views and ctools have been performed without error and no pending db updates were scheduled prior to this step.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>>>>>>>>>>> does not exist
>>>>>>>>>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>>>>>>>>>      ^
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> [...]
>>>>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I guess we have a fix for the first one, however that yields different errors:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> The table tripal_mviews exists but in the schema chado. I tried to set the search_path back:
>>>>>>>>>>>>>>>> ALTER USER user SET search_path TO public, chado;
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> However this yields other errors:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Cannot add field tripal_custom_tables.mview_id: table doesn't exist. [error]
>>>>>>>>>>>>>>>> [...]
>>>>>>>>>>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install on line 449
>>>>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install, line 449
>>>>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I searched and found http://sourceforge.net/p/gmod/mailman/message/32762105/ but that doesn't seem to fit.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Best
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Michael Dondrup
>>>>>>>>>>>>>>>> Researcher
>>>>>>>>>>>>>>>> Sea Lice Research Centre
>>>>>>>>>>>>>>>> Department of Informatics
>>>>>>>>>>>>>>>> University of Bergen
>>>>>>>>>>>>>>>> Thormøhlensgate 55, N-5008 Bergen,
>>>>>>>>>>>>>>>> Norway
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Full output of drush updatedb first iteration:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> $ drush updatedb
>>>>>>>>>>>>>>>> The following updates are pending:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> tripal_core module :
>>>>>>>>>>>>>>>> 7200 -   Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table
>>>>>>>>>>>>>>>> 7201 -   Fixes missing language for nodes and URL aliases. This may take awhile...
>>>>>>>>>>>>>>>> 7202 -   Adds a tripal_token_formats table for custom page titles and URL paths
>>>>>>>>>>>>>>>> 7203 -   Adds a tripal_toc table for customizing the table of contents on each Tripal page.
>>>>>>>>>>>>>>>> 7204 -   Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> tripal_organism module :
>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> tripal_cv module :
>>>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> tripal_contact module :
>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>>>>>>>>>> 7202 -   Updates path of tripal_contact OBO to be relative.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> tripal_bulk_loader module :
>>>>>>>>>>>>>>>> 7200 -   Implements hook_update_N().   Update to 7.x-2.0  -Cast tripal_bulk_loader.template_id to int field
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> tripal_library module :
>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_library when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> tripal_stock module :
>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_stock when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>> 7201 -   Add materialized views
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> tripal_project module :
>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_project when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> tripal_analysis module :
>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> tripal_featuremap module :
>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_featuremap when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>>>>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>>>>>>>>>> 7202 -   Fixes a typo when setting the default CV for the unittype_id field of the featuremap table.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> tripal_feature module :
>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_feature when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>>> 7202 -   Adds the temporary tables used for loading GFF files.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> tripal_views module :
>>>>>>>>>>>>>>>> 7200 -   Tripal Views Update for 7.x-2.0    - Add relationship_only field to tripal_views_join    - Add relationship_handler field to tripal_views_join
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> tripal_pub module :
>>>>>>>>>>>>>>>> 7202 -   Updates path of tripal_pub OBO to be relative.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Performed update: tripal_feature_update_7200 [ok]
>>>>>>>>>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>>>>>>>>>>> does not exist
>>>>>>>>>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>>>>>>>>>      ^
>>>>>>>>>>>>>>>> Performed update: tripal_feature_update_7201 [ok]
>>>>>>>>>>>>>>>> Performed update: tripal_featuremap_update_7200 [ok]
>>>>>>>>>>>>>>>> Performed update: tripal_featuremap_update_7201 [ok]
>>>>>>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Fatal error: Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>>>>> Finished performing updates. [ok]
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>>>>>>>>> Full output after setting search_path to public, chado
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Michael Dondrup-3
$ grep -re "function chado_get_node_title"
tripal_core/api/tripal_core.chado_nodes.title_and_path.inc:function chado_get_node_title($node)
so is the file name missing the '.api'?


On Jan 26, 2016, at 7:21 AM, Michael Dondrup wrote:

> Hi Stephen,
> I don't seem to have have this file,
> these are all the tripal_core api files I have.
>
>
> $  find . -iname "tripal_core*api*"
> ./tripal_core/api/tripal_core.chado_nodes.relationships.api.inc
> ./tripal_core/api/tripal_core.chado_variables.api.inc
> ./tripal_core/api/tripal_core.tripal_variables.api.inc
> ./tripal_core/api/tripal_core.chado_query.api.inc
> ./tripal_core/api/tripal_core.tripal.api.inc
> ./tripal_core/api/tripal_core.files.api.inc
> ./tripal_core/api/tripal_core.custom_tables.api.inc
> ./tripal_core/api/tripal_core.schema_v1.2.api.inc
> ./tripal_core/api/tripal_core.d3js.api.inc
> ./tripal_core/api/tripal_core.chado_nodes.api.inc
> ./tripal_core/api/tripal_core.chado_general.api.inc
> ./tripal_core/api/tripal_core.chado_schema.api.inc
> ./tripal_core/api/tripal_core.chado_nodes.dbxrefs.api.inc
> ./tripal_core/api/tripal_core.chado_nodes.properties.api.inc
> ./tripal_core/api/tripal_core.schema_v1.11.api.inc
> ./tripal_core/api/tripal_core.mviews.api.inc
> ./tripal_core/api/tripal_core.jobs.api.inc
>
>
> Michael
>
> On Jan 26, 2016, at 7:02 AM, Stephen Ficklin wrote:
>
>> Hmmm.....
>>
>> In your tripal/tripal_core/api directory there should be this file:
>>
>> tripal_core.chado_nodes.title_and_path.api.inc
>>
>> Note:  it should have 'api' in the name.  Is it there for you?
>>
>> Stephen
>>
>>
>> On 1/25/2016 9:51 PM, Michael Dondrup wrote:
>>> Hi,
>>>
>>> I pulled the latest 7.x-2.1-beta2 but the error is still the same.
>>>
>>> Michael
>>>
>>> On Jan 26, 2016, at 2:12 AM, Stephen Ficklin wrote:
>>>
>>>> Hi Michael,
>>>>
>>>> No need to apologize.   This was my mistake. I made a typo in the fix I made to get you passed the upgrade problems.  I fixed it, tested on my end and seems to be fine.  Please pull the most recent version of the development code from the git repository and you should have the fix.
>>>>
>>>> Please let me know if you have additional issues.
>>>>
>>>> Stephen
>>>>
>>>> On 1/25/2016 1:32 PM, Michael Dondrup wrote:
>>>>> Here we go, sorry to bother again.
>>>>> After enabling tripal_feature and most other tripal modules, when trying to access a feature I get:
>>>>>
>>>>> PHP Fatal error:  Call to undefined function chado_get_node_title() in /home/licebase/d7/sites/all/modules/tripal/tripal_feature/includes/tripal_feature.chado_node.inc on line 738, referer: https://localhost/tracker?page=1
>>>>>
>>>>> Best
>>>>> Michael
>>>>>
>>>>>
>>>>> On Jan 25, 2016, at 5:58 PM, Stephen Ficklin wrote:
>>>>>
>>>>>> Wonderful!  Yes, those warnings will unfortunately appear.  But, after you delete the view integrations (Step 17) they should be rebuilt and that message should go away.  I have made note of these warnings in the the upgrade instructions.
>>>>>>
>>>>>> Thanks for reaching out when you had issues.
>>>>>>
>>>>>> Stephen
>>>>>>
>>>>>> On 1/25/2016 6:20 AM, Michael Dondrup wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> thank you again. It worked!
>>>>>>>
>>>>>>> The dbupdate has been applied using the updated code.  There was only one repeated warning.
>>>>>>>
>>>>>>> in updating tripal_views
>>>>>>> [site https://...] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store relationship for studyprop_feature => feature when you should be using tripal_views_joins.
>>>>>>>
>>>>>>> I think we should take another snapshot here and start activating tripal core modules and see how that goes.
>>>>>>>
>>>>>>> Best
>>>>>>> Michael
>>>>>>>
>>>>>>>
>>>>>>> ----------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>> Below I will list the commands for our reference:
>>>>>>>
>>>>>>> # ALTER USER user SET search_path TO public; just to be shure
>>>>>>>
>>>>>>> ## applied taxonomy patch, but didn't start core update from scratch becasue we didn't have taxonomy errors
>>>>>>>
>>>>>>> ### starting from Snapshot step_12
>>>>>>>
>>>>>>> ## moved misplaced tables from chado to public in psql
>>>>>>>
>>>>>>> ALTER table chado.tripal_custom_tables set schema public;
>>>>>>> ALTER table chado.tripal_gff_temp set schema public;
>>>>>>> ALTER table chado.tripal_jobs set schema public;
>>>>>>> ALTER table chado.tripal_mviews set schema public;
>>>>>>> ALTER table chado.tripal_obo_temp set schema public;
>>>>>>>
>>>>>>>
>>>>>>> ### Step 13.
>>>>>>> drush pm-download views ctools
>>>>>>> drush updatedb
>>>>>>>
>>>>>>> drush pm-enable ctools views views_ui
>>>>>>>
>>>>>>> ## all OK Snapshot taken step_13
>>>>>>>
>>>>>>> ### Step 14. modified to get latest beta
>>>>>>>
>>>>>>> cd sites/all/modules
>>>>>>> git clone https://github.com/tripal/tripal.git -b 7.x-2.1-beta2
>>>>>>> # warning: Remote branch 7.x-2.1-beta2 not found in upstream origin, using HEAD instead
>>>>>>> cd tripal/
>>>>>>> ## 7.x-2.1-beta2 is a tag
>>>>>>> git checkout 7.x-2.1-beta2
>>>>>>>
>>>>>>> ### Step 15:
>>>>>>> drush updatedb
>>>>>>> ## all ok
>>>>>>>
>>>>>>> ### Step 16:
>>>>>>>
>>>>>>> drush pm-enable tripal_core
>>>>>>> ## all ok
>>>>>>> drush pm-enable tripal_views
>>>>>>>
>>>>>>> # repeated many times
>>>>>>> # [site https://...] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store
>>>>>>> # relationship for studyprop_feature => feature when you should be using tripal_views_joins.
>>>>>>>
>>>>>>> ### Step 17: Administration -> Tripal -> Views Integration -> click 'Delete All Integrations'
>>>>>>> # Successfully deleted all views integration.
>>>>>>> #Successfully rebuilt default Tripal Views Integrations
>>>>>>>
>>>>>>> ## Changed tripal_core.info to avoid update warnings
>>>>>>>> version = 7.x-2.1-beta2
>>>>>>> On Jan 24, 2016, at 11:17 AM, Michael Dondrup wrote:
>>>>>>>
>>>>>>>> Hi Stephen,
>>>>>>>> thank you so much for the quick response. I need to get our sysadmin involved to revert the database
>>>>>>>> to the correct snapshot. I hope I will be ready testing before the afternoon on monday.
>>>>>>>>
>>>>>>>> Michael
>>>>>>>>
>>>>>>>> On Jan 23, 2016, at 9:11 PM, Stephen Ficklin wrote:
>>>>>>>>
>>>>>>>>> Hi Michael,
>>>>>>>>>
>>>>>>>>> I found one irritating bug that should have been fixed for the beta1 release. I've fixed it but Drupal.org won't let me redo the release to include the fix, so I had to issue a new beta2 release.  Also, I'm not sure the command I gave you below to download Tripal will work, and I can't test it to make sure until Drupal creates the files.  So use this instead:
>>>>>>>>>
>>>>>>>>> git clone [hidden email]:tripal/tripal.git -b 7.x-2.1-beta2
>>>>>>>>>
>>>>>>>>> Stephen
>>>>>>>>>
>>>>>>>>> On 1/23/2016 11:02 AM, Stephen Ficklin wrote:
>>>>>>>>>> Hi Michael,
>>>>>>>>>>
>>>>>>>>>> The fixes are ready.  I have also adjusted the upgrade documentation to add a patch for a taxonomy bug that seems to occur for some people during upgrade.  I added a new step #10 to the upgrade documentation http://tripal.info/tutorials/v2.0/upgrade.    I also just released Tripal v2.1-beta1.  This is a precursor for our full Tripal v2.1 release (which will include support for Chado v1.3).
>>>>>>>>>>
>>>>>>>>>> So, in step #14 when it asks you download Tripal use this command instead
>>>>>>>>>>
>>>>>>>>>> drush pm-download tripal 7.x-2.1-beta1
>>>>>>>>>>
>>>>>>>>>> Drupal only rebuilds its releases at the end of the day so this beta release should be available tomorrow.
>>>>>>>>>>
>>>>>>>>>> I have tested an upgrade of Drupal 6 / Tripal v1 to Drupal 7 / Tripal v2 and it worked just fine without problems using this new beta1 version.
>>>>>>>>>>
>>>>>>>>>> Let me know if you have issues.
>>>>>>>>>>
>>>>>>>>>> Stephen
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 1/22/2016 10:26 AM, Michael Dondrup wrote:
>>>>>>>>>>> Hi Stephen,
>>>>>>>>>>>
>>>>>>>>>>> That would be great, we will just revert to the state directly after updating clean drupal core
>>>>>>>>>>> next week.
>>>>>>>>>>> Will php 5.3.3 and drush 6.7.0 be ok?
>>>>>>>>>>>
>>>>>>>>>>> Michael
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Jan 22, 2016, at 6:31 PM, Stephen Ficklin wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Michael,
>>>>>>>>>>>>
>>>>>>>>>>>> I believe I understand what the problem is.   I'm going to add a fix to Tripal v2.x (the development branch) and let you know when it's ready.  Can you use the development branch for testing your upgrade?  We're very close to releasing v2.1 so it should be stable enough to use.
>>>>>>>>>>>>
>>>>>>>>>>>> Stephen
>>>>>>>>>>>>
>>>>>>>>>>>> On 1/22/2016 2:39 AM, Michael Dondrup wrote:
>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>> we are still getting the 'undefined function errors' for functions that are in reality defined in the code of tripal:
>>>>>>>>>>>>> e.g. tripal_add_mview() or tripal_insert_obo(). These functions sometimes change erratically throughout the process.
>>>>>>>>>>>>> We were suspecting the drush version as we were initially using drush 5.7, we have therefore tested with other
>>>>>>>>>>>>> versions: 6.4 (as recommended in the documentation), 6.0, 6.7 (latest stable 6), 5.5.9. We also tried drush 7 branches, but
>>>>>>>>>>>>> these don't recognize a drupal site.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Drush install via composer, php version is PHP 5.3.3
>>>>>>>>>>>>>
>>>>>>>>>>>>> Each time we cleared the cache (drush cc all) and rebuilt the drush registry (drush rr). To no avail. As the process is a bit erratic
>>>>>>>>>>>>> I interpret this as caused by the sequence of php file inclusions.
>>>>>>>>>>>>>
>>>>>>>>>>>>> We have certainly hit a wall here, and would appreciate any input as the migration is somewhat urgent to cmplete.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thank you in advance for your help.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Michael
>>>>>>>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>>>>>> Full output below:
>>>>>>>>>>>>>
>>>>>>>>>>>>> $ drush updb
>>>>>>>>>>>>> Tripal_core        7204  Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>>>>>>>> Tripal_feature     7202  Adds the temporary tables used for loading GFF files.
>>>>>>>>>>>>> Tripal_pub         7202  Updates path of tripal_pub OBO to be relative.
>>>>>>>>>>>>> Tripal_stock       7201  Add materialized views
>>>>>>>>>>>>> Tripal_contact     7202  Updates path of tripal_contact OBO to be relative.
>>>>>>>>>>>>> Tripal_featuremap  7202  Fixes a typo when setting the default CV for the unittype_id field of the
>>>>>>>>>>>>>                         featuremap table.
>>>>>>>>>>>>> Do you wish to run all pending updates? (y/n): y
>>>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>>>>>>>>>>>
>>>>>>>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>>>>>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install, line 409
>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>> 'all' cache was cleared in self [success]
>>>>>>>>>>>>> Finished performing updates. [ok]
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Jan 21, 2016, at 9:32 PM, Michael Dondrup wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Stephen,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> thank your for your response, I think we are getting closer to the core of the problem.
>>>>>>>>>>>>>> Do you think this might cause also the 'call to undefined function' error?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Michael
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Jan 21, 2016, at 8:00 PM, Stephen Ficklin wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Michael,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> When you started your upgrade did you have the search_path set for the postrgreSQL user?
>>>>>>>>>>>>>> Yes we had re-set the search path to public only.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> (Step 3 in upgrade procedue http://tripal.info/tutorials/v2.0/upgrade).  If so, then perhaps some of the tables that should be in the 'public' schema in your D6 site are in the 'chado' schema and they shouldn't be.
>>>>>>>>>>>>>> I think this is the case: The following tripal* tables are in chado in our D6 system:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> licebase=> \dt chado.tripal*
>>>>>>>>>>>>>>              List of relations
>>>>>>>>>>>>>> Schema |         Name         | Type  |  Owner
>>>>>>>>>>>>>> --------+----------------------+-------+----------
>>>>>>>>>>>>>> chado  | tripal_custom_tables | table | lb_admin
>>>>>>>>>>>>>> chado  | tripal_gff_temp      | table | lb_admin
>>>>>>>>>>>>>> chado  | tripal_jobs          | table | lb_admin
>>>>>>>>>>>>>> chado  | tripal_mviews        | table | lb_admin
>>>>>>>>>>>>>> chado  | tripal_obo_temp      | table | lb_admin
>>>>>>>>>>>>>> (5 rows)
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> The following ones are in public
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> licebase=> \dt public.tripal*
>>>>>>>>>>>>>>                  List of relations
>>>>>>>>>>>>>> Schema |             Name             | Type  |  Owner
>>>>>>>>>>>>>> --------+------------------------------+-------+----------
>>>>>>>>>>>>>> public | tripal_analysis              | table | lb_admin
>>>>>>>>>>>>>> public | tripal_analysis_blast        | table | lb_admin
>>>>>>>>>>>>>> public | tripal_bulk_loader           | table | lb_admin
>>>>>>>>>>>>>> public | tripal_bulk_loader_constants | table | lb_admin
>>>>>>>>>>>>>> public | tripal_bulk_loader_inserted  | table | lb_admin
>>>>>>>>>>>>>> public | tripal_bulk_loader_template  | table | lb_admin
>>>>>>>>>>>>>> public | tripal_cv_obo                | table | lb_admin
>>>>>>>>>>>>>> public | tripal_feature_relagg        | table | lb_admin
>>>>>>>>>>>>>> public | tripal_pub_import            | table | lb_admin
>>>>>>>>>>>>>> public | tripal_views                 | table | lb_admin
>>>>>>>>>>>>>> public | tripal_views_field           | table | lb_admin
>>>>>>>>>>>>>> public | tripal_views_handlers        | table | lb_admin
>>>>>>>>>>>>>> public | tripal_views_join            | table | lb_admin
>>>>>>>>>>>>>> (13 rows)
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I do remember a bug at one point in one of our development versions that caused this.  If this is the case then it makes sense that you would have problems during the upgrade.   Do you have a backup of your D6 site database where you can look to see if those tables are in the 'chado' schema?
>>>>>>>>>>>>>> W are working on an identical copy, while the D6 Tripal1 system is still online and we have backups of each stage so we can start over. So I could just look it up in the
>>>>>>>>>>>>>> production system.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> If so, moving them to the 'public' schema and then retrying the upgrade may help.  If you do see some of these tables in the 'chado' schema but you're unsure if there are more that should also be moved feel free to send the list of tables in your 'chado' schema and I can let you know.
>>>>>>>>>>>>>> So should I first attempt move all those tripal* tables from chado to public? Funny enough this doesn't cause problems in the D6 system....
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Stephen
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On 1/21/2016 1:15 AM, Michael Dondrup wrote:
>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>> we fixed the first problem somehow the tripal_custom_tables table was created in chado schema. I moved it
>>>>>>>>>>>>>>>> ALTER TABLE tripal_custom_tables SET SCHEMA public;
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Leaving me with this error:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> This is weird because the function is certainly defined in tripal/tripal_cv/api/tripal_cv.api.inc:function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE)
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I have tried to drush cc all and even rebuilt the registry as described here: https://www.drupal.org/project/registry_rebuild
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> But to no avail. Anybody else having this problem?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I really appreciate your help.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Michael
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Jan 20, 2016, at 2:17 PM, Michael Dondrup wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> we are doing a test-run of the D6->7 migration of our site including a Tripal update, following http://tripal.info/tutorials/v2.0/upgrade
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> We are currently at step 14. Next, apply the Tripal updates: drush updatedb
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> All core updates, views and ctools have been performed without error and no pending db updates were scheduled prior to this step.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>>>>>>>>>>>> does not exist
>>>>>>>>>>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>>>>>>>>>>     ^
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> [...]
>>>>>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I guess we have a fix for the first one, however that yields different errors:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> The table tripal_mviews exists but in the schema chado. I tried to set the search_path back:
>>>>>>>>>>>>>>>>> ALTER USER user SET search_path TO public, chado;
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> However this yields other errors:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Cannot add field tripal_custom_tables.mview_id: table doesn't exist. [error]
>>>>>>>>>>>>>>>>> [...]
>>>>>>>>>>>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install on line 449
>>>>>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install, line 449
>>>>>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I searched and found http://sourceforge.net/p/gmod/mailman/message/32762105/ but that doesn't seem to fit.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Best
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Michael Dondrup
>>>>>>>>>>>>>>>>> Researcher
>>>>>>>>>>>>>>>>> Sea Lice Research Centre
>>>>>>>>>>>>>>>>> Department of Informatics
>>>>>>>>>>>>>>>>> University of Bergen
>>>>>>>>>>>>>>>>> Thormøhlensgate 55, N-5008 Bergen,
>>>>>>>>>>>>>>>>> Norway
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Full output of drush updatedb first iteration:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> $ drush updatedb
>>>>>>>>>>>>>>>>> The following updates are pending:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_core module :
>>>>>>>>>>>>>>>>> 7200 -   Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table
>>>>>>>>>>>>>>>>> 7201 -   Fixes missing language for nodes and URL aliases. This may take awhile...
>>>>>>>>>>>>>>>>> 7202 -   Adds a tripal_token_formats table for custom page titles and URL paths
>>>>>>>>>>>>>>>>> 7203 -   Adds a tripal_toc table for customizing the table of contents on each Tripal page.
>>>>>>>>>>>>>>>>> 7204 -   Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_organism module :
>>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_cv module :
>>>>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_contact module :
>>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>>>>>>>>>>> 7202 -   Updates path of tripal_contact OBO to be relative.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_bulk_loader module :
>>>>>>>>>>>>>>>>> 7200 -   Implements hook_update_N().   Update to 7.x-2.0  -Cast tripal_bulk_loader.template_id to int field
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_library module :
>>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_library when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_stock module :
>>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_stock when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>>> 7201 -   Add materialized views
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_project module :
>>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_project when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_analysis module :
>>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_featuremap module :
>>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_featuremap when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>>>>>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>>>>>>>>>>> 7202 -   Fixes a typo when setting the default CV for the unittype_id field of the featuremap table.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_feature module :
>>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_feature when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>>>> 7202 -   Adds the temporary tables used for loading GFF files.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_views module :
>>>>>>>>>>>>>>>>> 7200 -   Tripal Views Update for 7.x-2.0    - Add relationship_only field to tripal_views_join    - Add relationship_handler field to tripal_views_join
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_pub module :
>>>>>>>>>>>>>>>>> 7202 -   Updates path of tripal_pub OBO to be relative.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Performed update: tripal_feature_update_7200 [ok]
>>>>>>>>>>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>>>>>>>>>>>> does not exist
>>>>>>>>>>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>>>>>>>>>>     ^
>>>>>>>>>>>>>>>>> Performed update: tripal_feature_update_7201 [ok]
>>>>>>>>>>>>>>>>> Performed update: tripal_featuremap_update_7200 [ok]
>>>>>>>>>>>>>>>>> Performed update: tripal_featuremap_update_7201 [ok]
>>>>>>>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Fatal error: Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>>>>>> Finished performing updates. [ok]
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>>>>>>>>>> Full output after setting search_path to public, chado
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Stephen Ficklin-2
In reply to this post by Michael Dondrup-3
Odd... that file shouldn't be missing.  If you execute these command
does it retrieve the file?

git checkout 7.x-2.x
git pull

Stephen

On 1/25/2016 10:21 PM, Michael Dondrup wrote:

> Hi Stephen,
> I don't seem to have have this file,
> these are all the tripal_core api files I have.
>
>
> $  find . -iname "tripal_core*api*"
> ./tripal_core/api/tripal_core.chado_nodes.relationships.api.inc
> ./tripal_core/api/tripal_core.chado_variables.api.inc
> ./tripal_core/api/tripal_core.tripal_variables.api.inc
> ./tripal_core/api/tripal_core.chado_query.api.inc
> ./tripal_core/api/tripal_core.tripal.api.inc
> ./tripal_core/api/tripal_core.files.api.inc
> ./tripal_core/api/tripal_core.custom_tables.api.inc
> ./tripal_core/api/tripal_core.schema_v1.2.api.inc
> ./tripal_core/api/tripal_core.d3js.api.inc
> ./tripal_core/api/tripal_core.chado_nodes.api.inc
> ./tripal_core/api/tripal_core.chado_general.api.inc
> ./tripal_core/api/tripal_core.chado_schema.api.inc
> ./tripal_core/api/tripal_core.chado_nodes.dbxrefs.api.inc
> ./tripal_core/api/tripal_core.chado_nodes.properties.api.inc
> ./tripal_core/api/tripal_core.schema_v1.11.api.inc
> ./tripal_core/api/tripal_core.mviews.api.inc
> ./tripal_core/api/tripal_core.jobs.api.inc
>
>
> Michael
>
> On Jan 26, 2016, at 7:02 AM, Stephen Ficklin wrote:
>
>> Hmmm.....
>>
>> In your tripal/tripal_core/api directory there should be this file:
>>
>> tripal_core.chado_nodes.title_and_path.api.inc
>>
>> Note:  it should have 'api' in the name.  Is it there for you?
>>
>> Stephen
>>
>>
>> On 1/25/2016 9:51 PM, Michael Dondrup wrote:
>>> Hi,
>>>
>>> I pulled the latest 7.x-2.1-beta2 but the error is still the same.
>>>
>>> Michael
>>>
>>> On Jan 26, 2016, at 2:12 AM, Stephen Ficklin wrote:
>>>
>>>> Hi Michael,
>>>>
>>>> No need to apologize.   This was my mistake. I made a typo in the fix I made to get you passed the upgrade problems.  I fixed it, tested on my end and seems to be fine.  Please pull the most recent version of the development code from the git repository and you should have the fix.
>>>>
>>>> Please let me know if you have additional issues.
>>>>
>>>> Stephen
>>>>
>>>> On 1/25/2016 1:32 PM, Michael Dondrup wrote:
>>>>> Here we go, sorry to bother again.
>>>>> After enabling tripal_feature and most other tripal modules, when trying to access a feature I get:
>>>>>
>>>>> PHP Fatal error:  Call to undefined function chado_get_node_title() in /home/licebase/d7/sites/all/modules/tripal/tripal_feature/includes/tripal_feature.chado_node.inc on line 738, referer: https://localhost/tracker?page=1
>>>>>
>>>>> Best
>>>>> Michael
>>>>>
>>>>>
>>>>> On Jan 25, 2016, at 5:58 PM, Stephen Ficklin wrote:
>>>>>
>>>>>> Wonderful!  Yes, those warnings will unfortunately appear.  But, after you delete the view integrations (Step 17) they should be rebuilt and that message should go away.  I have made note of these warnings in the the upgrade instructions.
>>>>>>
>>>>>> Thanks for reaching out when you had issues.
>>>>>>
>>>>>> Stephen
>>>>>>
>>>>>> On 1/25/2016 6:20 AM, Michael Dondrup wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> thank you again. It worked!
>>>>>>>
>>>>>>> The dbupdate has been applied using the updated code.  There was only one repeated warning.
>>>>>>>
>>>>>>> in updating tripal_views
>>>>>>>   [site https://...] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store relationship for studyprop_feature => feature when you should be using tripal_views_joins.
>>>>>>>
>>>>>>> I think we should take another snapshot here and start activating tripal core modules and see how that goes.
>>>>>>>
>>>>>>> Best
>>>>>>> Michael
>>>>>>>
>>>>>>>
>>>>>>> ----------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>> Below I will list the commands for our reference:
>>>>>>>
>>>>>>> # ALTER USER user SET search_path TO public; just to be shure
>>>>>>>
>>>>>>> ## applied taxonomy patch, but didn't start core update from scratch becasue we didn't have taxonomy errors
>>>>>>>
>>>>>>> ### starting from Snapshot step_12
>>>>>>>
>>>>>>> ## moved misplaced tables from chado to public in psql
>>>>>>>
>>>>>>> ALTER table chado.tripal_custom_tables set schema public;
>>>>>>> ALTER table chado.tripal_gff_temp set schema public;
>>>>>>> ALTER table chado.tripal_jobs set schema public;
>>>>>>> ALTER table chado.tripal_mviews set schema public;
>>>>>>> ALTER table chado.tripal_obo_temp set schema public;
>>>>>>>
>>>>>>>
>>>>>>> ### Step 13.
>>>>>>> drush pm-download views ctools
>>>>>>> drush updatedb
>>>>>>>
>>>>>>> drush pm-enable ctools views views_ui
>>>>>>>
>>>>>>> ## all OK Snapshot taken step_13
>>>>>>>
>>>>>>> ### Step 14. modified to get latest beta
>>>>>>>
>>>>>>> cd sites/all/modules
>>>>>>> git clone https://github.com/tripal/tripal.git -b 7.x-2.1-beta2
>>>>>>> # warning: Remote branch 7.x-2.1-beta2 not found in upstream origin, using HEAD instead
>>>>>>> cd tripal/
>>>>>>> ## 7.x-2.1-beta2 is a tag
>>>>>>> git checkout 7.x-2.1-beta2
>>>>>>>
>>>>>>> ### Step 15:
>>>>>>> drush updatedb
>>>>>>> ## all ok
>>>>>>>
>>>>>>> ### Step 16:
>>>>>>>
>>>>>>> drush pm-enable tripal_core
>>>>>>> ## all ok
>>>>>>> drush pm-enable tripal_views
>>>>>>>
>>>>>>> # repeated many times
>>>>>>> # [site https://...] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store
>>>>>>> # relationship for studyprop_feature => feature when you should be using tripal_views_joins.
>>>>>>>
>>>>>>> ### Step 17: Administration -> Tripal -> Views Integration -> click 'Delete All Integrations'
>>>>>>> # Successfully deleted all views integration.
>>>>>>> #Successfully rebuilt default Tripal Views Integrations
>>>>>>>
>>>>>>> ## Changed tripal_core.info to avoid update warnings
>>>>>>>> version = 7.x-2.1-beta2
>>>>>>> On Jan 24, 2016, at 11:17 AM, Michael Dondrup wrote:
>>>>>>>
>>>>>>>> Hi Stephen,
>>>>>>>> thank you so much for the quick response. I need to get our sysadmin involved to revert the database
>>>>>>>> to the correct snapshot. I hope I will be ready testing before the afternoon on monday.
>>>>>>>>
>>>>>>>> Michael
>>>>>>>>
>>>>>>>> On Jan 23, 2016, at 9:11 PM, Stephen Ficklin wrote:
>>>>>>>>
>>>>>>>>> Hi Michael,
>>>>>>>>>
>>>>>>>>> I found one irritating bug that should have been fixed for the beta1 release. I've fixed it but Drupal.org won't let me redo the release to include the fix, so I had to issue a new beta2 release.  Also, I'm not sure the command I gave you below to download Tripal will work, and I can't test it to make sure until Drupal creates the files.  So use this instead:
>>>>>>>>>
>>>>>>>>> git clone [hidden email]:tripal/tripal.git -b 7.x-2.1-beta2
>>>>>>>>>
>>>>>>>>> Stephen
>>>>>>>>>
>>>>>>>>> On 1/23/2016 11:02 AM, Stephen Ficklin wrote:
>>>>>>>>>> Hi Michael,
>>>>>>>>>>
>>>>>>>>>> The fixes are ready.  I have also adjusted the upgrade documentation to add a patch for a taxonomy bug that seems to occur for some people during upgrade.  I added a new step #10 to the upgrade documentation http://tripal.info/tutorials/v2.0/upgrade.    I also just released Tripal v2.1-beta1.  This is a precursor for our full Tripal v2.1 release (which will include support for Chado v1.3).
>>>>>>>>>>
>>>>>>>>>> So, in step #14 when it asks you download Tripal use this command instead
>>>>>>>>>>
>>>>>>>>>> drush pm-download tripal 7.x-2.1-beta1
>>>>>>>>>>
>>>>>>>>>> Drupal only rebuilds its releases at the end of the day so this beta release should be available tomorrow.
>>>>>>>>>>
>>>>>>>>>> I have tested an upgrade of Drupal 6 / Tripal v1 to Drupal 7 / Tripal v2 and it worked just fine without problems using this new beta1 version.
>>>>>>>>>>
>>>>>>>>>> Let me know if you have issues.
>>>>>>>>>>
>>>>>>>>>> Stephen
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 1/22/2016 10:26 AM, Michael Dondrup wrote:
>>>>>>>>>>> Hi Stephen,
>>>>>>>>>>>
>>>>>>>>>>> That would be great, we will just revert to the state directly after updating clean drupal core
>>>>>>>>>>> next week.
>>>>>>>>>>> Will php 5.3.3 and drush 6.7.0 be ok?
>>>>>>>>>>>
>>>>>>>>>>> Michael
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Jan 22, 2016, at 6:31 PM, Stephen Ficklin wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Michael,
>>>>>>>>>>>>
>>>>>>>>>>>> I believe I understand what the problem is.   I'm going to add a fix to Tripal v2.x (the development branch) and let you know when it's ready.  Can you use the development branch for testing your upgrade?  We're very close to releasing v2.1 so it should be stable enough to use.
>>>>>>>>>>>>
>>>>>>>>>>>> Stephen
>>>>>>>>>>>>
>>>>>>>>>>>> On 1/22/2016 2:39 AM, Michael Dondrup wrote:
>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>> we are still getting the 'undefined function errors' for functions that are in reality defined in the code of tripal:
>>>>>>>>>>>>> e.g. tripal_add_mview() or tripal_insert_obo(). These functions sometimes change erratically throughout the process.
>>>>>>>>>>>>> We were suspecting the drush version as we were initially using drush 5.7, we have therefore tested with other
>>>>>>>>>>>>> versions: 6.4 (as recommended in the documentation), 6.0, 6.7 (latest stable 6), 5.5.9. We also tried drush 7 branches, but
>>>>>>>>>>>>> these don't recognize a drupal site.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Drush install via composer, php version is PHP 5.3.3
>>>>>>>>>>>>>
>>>>>>>>>>>>> Each time we cleared the cache (drush cc all) and rebuilt the drush registry (drush rr). To no avail. As the process is a bit erratic
>>>>>>>>>>>>> I interpret this as caused by the sequence of php file inclusions.
>>>>>>>>>>>>>
>>>>>>>>>>>>> We have certainly hit a wall here, and would appreciate any input as the migration is somewhat urgent to cmplete.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thank you in advance for your help.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Michael
>>>>>>>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>>>>>> Full output below:
>>>>>>>>>>>>>
>>>>>>>>>>>>> $ drush updb
>>>>>>>>>>>>> Tripal_core        7204  Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>>>>>>>> Tripal_feature     7202  Adds the temporary tables used for loading GFF files.
>>>>>>>>>>>>> Tripal_pub         7202  Updates path of tripal_pub OBO to be relative.
>>>>>>>>>>>>> Tripal_stock       7201  Add materialized views
>>>>>>>>>>>>> Tripal_contact     7202  Updates path of tripal_contact OBO to be relative.
>>>>>>>>>>>>> Tripal_featuremap  7202  Fixes a typo when setting the default CV for the unittype_id field of the
>>>>>>>>>>>>>                           featuremap table.
>>>>>>>>>>>>> Do you wish to run all pending updates? (y/n): y
>>>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>>>>>>>>>>>
>>>>>>>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install on line 409
>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error.                              [error]
>>>>>>>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_contact/tripal_contact.install, line 409
>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>> 'all' cache was cleared in self [success]
>>>>>>>>>>>>> Finished performing updates. [ok]
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Jan 21, 2016, at 9:32 PM, Michael Dondrup wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Stephen,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> thank your for your response, I think we are getting closer to the core of the problem.
>>>>>>>>>>>>>> Do you think this might cause also the 'call to undefined function' error?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Michael
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Jan 21, 2016, at 8:00 PM, Stephen Ficklin wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Michael,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> When you started your upgrade did you have the search_path set for the postrgreSQL user?
>>>>>>>>>>>>>> Yes we had re-set the search path to public only.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> (Step 3 in upgrade procedue http://tripal.info/tutorials/v2.0/upgrade).  If so, then perhaps some of the tables that should be in the 'public' schema in your D6 site are in the 'chado' schema and they shouldn't be.
>>>>>>>>>>>>>> I think this is the case: The following tripal* tables are in chado in our D6 system:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> licebase=> \dt chado.tripal*
>>>>>>>>>>>>>>                List of relations
>>>>>>>>>>>>>> Schema |         Name         | Type  |  Owner
>>>>>>>>>>>>>> --------+----------------------+-------+----------
>>>>>>>>>>>>>> chado  | tripal_custom_tables | table | lb_admin
>>>>>>>>>>>>>> chado  | tripal_gff_temp      | table | lb_admin
>>>>>>>>>>>>>> chado  | tripal_jobs          | table | lb_admin
>>>>>>>>>>>>>> chado  | tripal_mviews        | table | lb_admin
>>>>>>>>>>>>>> chado  | tripal_obo_temp      | table | lb_admin
>>>>>>>>>>>>>> (5 rows)
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> The following ones are in public
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> licebase=> \dt public.tripal*
>>>>>>>>>>>>>>                    List of relations
>>>>>>>>>>>>>> Schema |             Name             | Type  |  Owner
>>>>>>>>>>>>>> --------+------------------------------+-------+----------
>>>>>>>>>>>>>> public | tripal_analysis              | table | lb_admin
>>>>>>>>>>>>>> public | tripal_analysis_blast        | table | lb_admin
>>>>>>>>>>>>>> public | tripal_bulk_loader           | table | lb_admin
>>>>>>>>>>>>>> public | tripal_bulk_loader_constants | table | lb_admin
>>>>>>>>>>>>>> public | tripal_bulk_loader_inserted  | table | lb_admin
>>>>>>>>>>>>>> public | tripal_bulk_loader_template  | table | lb_admin
>>>>>>>>>>>>>> public | tripal_cv_obo                | table | lb_admin
>>>>>>>>>>>>>> public | tripal_feature_relagg        | table | lb_admin
>>>>>>>>>>>>>> public | tripal_pub_import            | table | lb_admin
>>>>>>>>>>>>>> public | tripal_views                 | table | lb_admin
>>>>>>>>>>>>>> public | tripal_views_field           | table | lb_admin
>>>>>>>>>>>>>> public | tripal_views_handlers        | table | lb_admin
>>>>>>>>>>>>>> public | tripal_views_join            | table | lb_admin
>>>>>>>>>>>>>> (13 rows)
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I do remember a bug at one point in one of our development versions that caused this.  If this is the case then it makes sense that you would have problems during the upgrade.   Do you have a backup of your D6 site database where you can look to see if those tables are in the 'chado' schema?
>>>>>>>>>>>>>> W are working on an identical copy, while the D6 Tripal1 system is still online and we have backups of each stage so we can start over. So I could just look it up in the
>>>>>>>>>>>>>> production system.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> If so, moving them to the 'public' schema and then retrying the upgrade may help.  If you do see some of these tables in the 'chado' schema but you're unsure if there are more that should also be moved feel free to send the list of tables in your 'chado' schema and I can let you know.
>>>>>>>>>>>>>> So should I first attempt move all those tripal* tables from chado to public? Funny enough this doesn't cause problems in the D6 system....
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Stephen
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On 1/21/2016 1:15 AM, Michael Dondrup wrote:
>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>> we fixed the first problem somehow the tripal_custom_tables table was created in chado schema. I moved it
>>>>>>>>>>>>>>>> ALTER TABLE tripal_custom_tables SET SCHEMA public;
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Leaving me with this error:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> This is weird because the function is certainly defined in tripal/tripal_cv/api/tripal_cv.api.inc:function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE)
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I have tried to drush cc all and even rebuilt the registry as described here: https://www.drupal.org/project/registry_rebuild
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> But to no avail. Anybody else having this problem?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I really appreciate your help.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Michael
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Jan 20, 2016, at 2:17 PM, Michael Dondrup wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> we are doing a test-run of the D6->7 migration of our site including a Tripal update, following http://tripal.info/tutorials/v2.0/upgrade
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> We are currently at step 14. Next, apply the Tripal updates: drush updatedb
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> All core updates, views and ctools have been performed without error and no pending db updates were scheduled prior to this step.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>>>>>>>>>>>> does not exist
>>>>>>>>>>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>>>>>>>>>>       ^
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> [...]
>>>>>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I guess we have a fix for the first one, however that yields different errors:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> The table tripal_mviews exists but in the schema chado. I tried to set the search_path back:
>>>>>>>>>>>>>>>>> ALTER USER user SET search_path TO public, chado;
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> However this yields other errors:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Cannot add field tripal_custom_tables.mview_id: table doesn't exist. [error]
>>>>>>>>>>>>>>>>> [...]
>>>>>>>>>>>>>>>>> Fatal error: Call to undefined function tripal_insert_obo() in /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install on line 449
>>>>>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>>>>>>> Error: Call to undefined function tripal_insert_obo() in
>>>>>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_pub/tripal_pub.install, line 449
>>>>>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I searched and found http://sourceforge.net/p/gmod/mailman/message/32762105/ but that doesn't seem to fit.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Best
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Michael Dondrup
>>>>>>>>>>>>>>>>> Researcher
>>>>>>>>>>>>>>>>> Sea Lice Research Centre
>>>>>>>>>>>>>>>>> Department of Informatics
>>>>>>>>>>>>>>>>> University of Bergen
>>>>>>>>>>>>>>>>> Thormøhlensgate 55, N-5008 Bergen,
>>>>>>>>>>>>>>>>> Norway
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Full output of drush updatedb first iteration:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> $ drush updatedb
>>>>>>>>>>>>>>>>> The following updates are pending:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_core module :
>>>>>>>>>>>>>>>>> 7200 -   Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table
>>>>>>>>>>>>>>>>> 7201 -   Fixes missing language for nodes and URL aliases. This may take awhile...
>>>>>>>>>>>>>>>>> 7202 -   Adds a tripal_token_formats table for custom page titles and URL paths
>>>>>>>>>>>>>>>>> 7203 -   Adds a tripal_toc table for customizing the table of contents on each Tripal page.
>>>>>>>>>>>>>>>>> 7204 -   Adds the tripal_variable_terms and a tripal_node_variables tables
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_organism module :
>>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_cv module :
>>>>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_contact module :
>>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>>>>>>>>>>> 7202 -   Updates path of tripal_contact OBO to be relative.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_bulk_loader module :
>>>>>>>>>>>>>>>>> 7200 -   Implements hook_update_N().   Update to 7.x-2.0  -Cast tripal_bulk_loader.template_id to int field
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_library module :
>>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_library when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_stock module :
>>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_stock when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>>> 7201 -   Add materialized views
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_project module :
>>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_project when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_analysis module :
>>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
>>>>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_featuremap module :
>>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_featuremap when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>>>>>>>>>>>> 7201 -   Adds missing foreign key constraints
>>>>>>>>>>>>>>>>> 7202 -   Fixes a typo when setting the default CV for the unittype_id field of the featuremap table.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_feature module :
>>>>>>>>>>>>>>>>> 7200 -   This is the required update for tripal_feature when upgrading from Drupal core API 6.x.  This update may take some time to complete.
>>>>>>>>>>>>>>>>> 7201 -   Fixes an error with the materialized view installation
>>>>>>>>>>>>>>>>> 7202 -   Adds the temporary tables used for loading GFF files.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_views module :
>>>>>>>>>>>>>>>>> 7200 -   Tripal Views Update for 7.x-2.0    - Add relationship_only field to tripal_views_join    - Add relationship_handler field to tripal_views_join
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> tripal_pub module :
>>>>>>>>>>>>>>>>> 7202 -   Updates path of tripal_pub OBO to be relative.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Performed update: tripal_feature_update_7200 [ok]
>>>>>>>>>>>>>>>>> Failed to complete updateSQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "tripal_mviews"   [error]
>>>>>>>>>>>>>>>>> does not exist
>>>>>>>>>>>>>>>>> LINE 3: tripal_mviews tm
>>>>>>>>>>>>>>>>>       ^
>>>>>>>>>>>>>>>>> Performed update: tripal_feature_update_7201 [ok]
>>>>>>>>>>>>>>>>> Performed update: tripal_featuremap_update_7200 [ok]
>>>>>>>>>>>>>>>>> Performed update: tripal_featuremap_update_7201 [ok]
>>>>>>>>>>>>>>>>> PHP Fatal error:  Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Fatal error: Call to undefined function tripal_set_default_cv() in /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install on line 655
>>>>>>>>>>>>>>>>> Drush command terminated abnormally due to an unrecoverable error. [error]
>>>>>>>>>>>>>>>>> Error: Call to undefined function tripal_set_default_cv() in
>>>>>>>>>>>>>>>>> /home/licebase/d7/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install, line 655
>>>>>>>>>>>>>>>>> The external command could not be executed due to an application error.                         [error]
>>>>>>>>>>>>>>>>> Finished performing updates. [ok]
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> ---------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>>>>>>>>>> Full output after setting search_path to public, chado
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Michael Dondrup-3
Sorry I was still on 7.x-2.1-beta2


On Jan 26, 2016, at 7:27 AM, Stephen Ficklin wrote:

> git checkout 7.x-2.x
> git pull

Now it is workin for me too! THank you

------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: Tripal 2 update errors

Stephen Ficklin-2
Oh good.  Sorry about the beta releases not working, but I guess that's
why they're beta.


On 1/25/2016 10:32 PM, Michael Dondrup wrote:
> Sorry I was still on 7.x-2.1-beta2
>
>
> On Jan 26, 2016, at 7:27 AM, Stephen Ficklin wrote:
>
>> git checkout 7.x-2.x
>> git pull
> Now it is workin for me too! THank you


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal