[Gmod-tripal-devel] failures when updating from drupal 6 to 7

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[Gmod-tripal-devel] failures when updating from drupal 6 to 7

Scott Cain
Hi Stephen and all,

After updating my Chado instance from 1.23 to 1.31 I tried to update to Tripal 2/Drupal 7, but I got these database errors.  Do you think these are due to the Chado update or something else?  It looks like it's trying to insert data that is already in the database.  If so, shouldn't the update script realize that and not fail?

Thanks,
Scott


The following updates returned messages

tripal_organism module

Update #7200

  • Failed: DrupalUpdateException: Failed to add organism_property vocabulary: SQLSTATE[23505]: Unique violation: 7 ERROR: duplicate key value violates unique constraint "tripal_cv_defaults_tripal_cv_defaults_unq1_key" DETAIL: Key (table_name, field_name, cv_id)=(organismprop, type_id, 29) already exists. in tripal_organism_update_7200() (line 156 of /var/www/sites/all/modules/tripal/tripal_organism/tripal_organism.install).

tripal_feature module

Update #7200

  • Failed: DrupalUpdateException: Could not move feature taxonomy terms: SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "field_data_taxonomyextra" does not exist LINE 5: FROM field_data_taxonomyextra ^ in tripal_feature_update_7200() (line 368 of /var/www/sites/all/modules/tripal/tripal_feature/tripal_feature.install).

tripal_analysis module

Update #7200

  • Failed: DrupalUpdateException: Failed to add analysis_property vocabulary: SQLSTATE[23505]: Unique violation: 7 ERROR: duplicate key value violates unique constraint "tripal_cv_defaults_tripal_cv_defaults_unq1_key" DETAIL: Key (table_name, field_name, cv_id)=(analysisprop, type_id, 28) already exists. in tripal_analysis_update_7200() (line 313 of /var/www/sites/all/modules/tripal/tripal_analysis/tripal_analysis.install).

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: [Gmod-tripal-devel] failures when updating from drupal 6 to 7

Stephen Ficklin-2
HI Scott,

Thanks for pointing out this problem.  There indeed were a few bugs in the update code that you hit on.  I've applied some fixes and committed those to the development branch (7.x-2.x).   If you retry the upgrade let me know if you still have issues.

Thanks,
Stephen


On 10/23/2015 11:09 AM, Scott Cain wrote:
Hi Stephen and all,

After updating my Chado instance from 1.23 to 1.31 I tried to update to Tripal 2/Drupal 7, but I got these database errors.  Do you think these are due to the Chado update or something else?  It looks like it's trying to insert data that is already in the database.  If so, shouldn't the update script realize that and not fail?

Thanks,
Scott


The following updates returned messages

tripal_organism module

Update #7200

  • Failed: DrupalUpdateException: Failed to add organism_property vocabulary: SQLSTATE[23505]: Unique violation: 7 ERROR: duplicate key value violates unique constraint "tripal_cv_defaults_tripal_cv_defaults_unq1_key" DETAIL: Key (table_name, field_name, cv_id)=(organismprop, type_id, 29) already exists. in tripal_organism_update_7200() (line 156 of /var/www/sites/all/modules/tripal/tripal_organism/tripal_organism.install).

tripal_feature module

Update #7200

  • Failed: DrupalUpdateException: Could not move feature taxonomy terms: SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "field_data_taxonomyextra" does not exist LINE 5: FROM field_data_taxonomyextra ^ in tripal_feature_update_7200() (line 368 of /var/www/sites/all/modules/tripal/tripal_feature/tripal_feature.install).

tripal_analysis module

Update #7200

  • Failed: DrupalUpdateException: Failed to add analysis_property vocabulary: SQLSTATE[23505]: Unique violation: 7 ERROR: duplicate key value violates unique constraint "tripal_cv_defaults_tripal_cv_defaults_unq1_key" DETAIL: Key (table_name, field_name, cv_id)=(analysisprop, type_id, 28) already exists. in tripal_analysis_update_7200() (line 313 of /var/www/sites/all/modules/tripal/tripal_analysis/tripal_analysis.install).

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


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Re: [Gmod-tripal-devel] failures when updating from drupal 6 to 7

Scott Cain
Hi Stephen,

It seems to be going a little smoother now, though when I enable the views module, I get LOTS off warnings like this one:

[site http://default] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store relationship for featuremap_pub => pub when you should be using tripal_views_joins.

Did I miss an update step?




On Mon, Oct 26, 2015 at 2:35 PM, Stephen Ficklin <[hidden email]> wrote:
HI Scott,

Thanks for pointing out this problem.  There indeed were a few bugs in the update code that you hit on.  I've applied some fixes and committed those to the development branch (7.x-2.x).   If you retry the upgrade let me know if you still have issues.

Thanks,
Stephen



On 10/23/2015 11:09 AM, Scott Cain wrote:
Hi Stephen and all,

After updating my Chado instance from 1.23 to 1.31 I tried to update to Tripal 2/Drupal 7, but I got these database errors.  Do you think these are due to the Chado update or something else?  It looks like it's trying to insert data that is already in the database.  If so, shouldn't the update script realize that and not fail?

Thanks,
Scott


The following updates returned messages

tripal_organism module

Update #7200

  • Failed: DrupalUpdateException: Failed to add organism_property vocabulary: SQLSTATE[23505]: Unique violation: 7 ERROR: duplicate key value violates unique constraint "tripal_cv_defaults_tripal_cv_defaults_unq1_key" DETAIL: Key (table_name, field_name, cv_id)=(organismprop, type_id, 29) already exists. in tripal_organism_update_7200() (line 156 of /var/www/sites/all/modules/tripal/tripal_organism/tripal_organism.install).

tripal_feature module

Update #7200

  • Failed: DrupalUpdateException: Could not move feature taxonomy terms: SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "field_data_taxonomyextra" does not exist LINE 5: FROM field_data_taxonomyextra ^ in tripal_feature_update_7200() (line 368 of /var/www/sites/all/modules/tripal/tripal_feature/tripal_feature.install).

tripal_analysis module

Update #7200

  • Failed: DrupalUpdateException: Failed to add analysis_property vocabulary: SQLSTATE[23505]: Unique violation: 7 ERROR: duplicate key value violates unique constraint "tripal_cv_defaults_tripal_cv_defaults_unq1_key" DETAIL: Key (table_name, field_name, cv_id)=(analysisprop, type_id, 28) already exists. in tripal_analysis_update_7200() (line 313 of /var/www/sites/all/modules/tripal/tripal_analysis/tripal_analysis.install).

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: [Gmod-tripal-devel] failures when updating from drupal 6 to 7

Scott Cain
Hi Stephen,

I seem to have fixed the deprecated issue "by accident" while I was doing other things (turning various things on and off and whatnot).  Anyway, it seems to have gone away, possibly by my jumping ahead in the the upgrade guide; hard to say what did it though.



On Mon, Oct 26, 2015 at 4:52 PM, Scott Cain <[hidden email]> wrote:
Hi Stephen,

It seems to be going a little smoother now, though when I enable the views module, I get LOTS off warnings like this one:

[site http://default] [TRIPAL NOTICE] [TRIPAL_VIEWS] DEPRECATED: Currently using tripal_views_handlers to store relationship for featuremap_pub => pub when you should be using tripal_views_joins.

Did I miss an update step?




On Mon, Oct 26, 2015 at 2:35 PM, Stephen Ficklin <[hidden email]> wrote:
HI Scott,

Thanks for pointing out this problem.  There indeed were a few bugs in the update code that you hit on.  I've applied some fixes and committed those to the development branch (7.x-2.x).   If you retry the upgrade let me know if you still have issues.

Thanks,
Stephen



On 10/23/2015 11:09 AM, Scott Cain wrote:
Hi Stephen and all,

After updating my Chado instance from 1.23 to 1.31 I tried to update to Tripal 2/Drupal 7, but I got these database errors.  Do you think these are due to the Chado update or something else?  It looks like it's trying to insert data that is already in the database.  If so, shouldn't the update script realize that and not fail?

Thanks,
Scott


The following updates returned messages

tripal_organism module

Update #7200

  • Failed: DrupalUpdateException: Failed to add organism_property vocabulary: SQLSTATE[23505]: Unique violation: 7 ERROR: duplicate key value violates unique constraint "tripal_cv_defaults_tripal_cv_defaults_unq1_key" DETAIL: Key (table_name, field_name, cv_id)=(organismprop, type_id, 29) already exists. in tripal_organism_update_7200() (line 156 of /var/www/sites/all/modules/tripal/tripal_organism/tripal_organism.install).

tripal_feature module

Update #7200

  • Failed: DrupalUpdateException: Could not move feature taxonomy terms: SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "field_data_taxonomyextra" does not exist LINE 5: FROM field_data_taxonomyextra ^ in tripal_feature_update_7200() (line 368 of /var/www/sites/all/modules/tripal/tripal_feature/tripal_feature.install).

tripal_analysis module

Update #7200

  • Failed: DrupalUpdateException: Failed to add analysis_property vocabulary: SQLSTATE[23505]: Unique violation: 7 ERROR: duplicate key value violates unique constraint "tripal_cv_defaults_tripal_cv_defaults_unq1_key" DETAIL: Key (table_name, field_name, cv_id)=(analysisprop, type_id, 28) already exists. in tripal_analysis_update_7200() (line 313 of /var/www/sites/all/modules/tripal/tripal_analysis/tripal_analysis.install).

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------


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Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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