[Loris-dev] Errors upgrading LORIS v22.0.4 to v23.0.0

Mon Jan 18 11:58:26 EST 2021

Hi Alfredo,

Looking at the patch it looks like both of the sections that have the error
message are doing a subselect for the user named "admin" in a part where
it's trying to give newly created permissions to the admin user so that
they can be selected in the frontend. Do you have a user named "admin" or
did you rename it?

In either case, I don't think it will affect your upgrade. You can manually
give the electrophysiology_browser_view_site,
electrophysiology_browser_view_allsites, module_manager_view, and
module_manager_edit to whichever user you use to manage user accounts based
on the insert statements in the script by changing "admin" to whatever
username you're using. If you don't plan on using the electrophysiology
browser or module manager modules, I don't think anything else should be
affected other than the ability to grant the permissions in the frontend.
The permissions themselves were created so the code shouldn't break.

On Fri, Jan 15, 2021 at 9:38 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Dear Loris DevTeam,
>
> I am upgrading LORIS to the last version 23.0.0. While executing the SQL
> patch I got the following output with errors (see below). I have followed
> all the upgrading steps. Any ideas on what can be missing?
>
> Regards,
> Alfredo.
>
> ===
> mysql> source /home/bic/moralf/22.0_To_23.0_upgrade.sql
>
> +------------------------------------------------------------------------------------+
> | Running:
> SQL/New_patches/2018-05-18-adding_physiological_all_sites_permissions.sql |
>
> +------------------------------------------------------------------------------------+
> | Running:
> SQL/New_patches/2018-05-18-adding_physiological_all_sites_permissions.sql |
>
> +------------------------------------------------------------------------------------+
> 1 row in set (0.01 sec)
>
> Query OK, 1 row affected (0.03 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> ERROR 1048 (23000): Column 'userID' cannot be null
> ERROR 1048 (23000): Column 'userID' cannot be null
> +---------------------------------------------------------------------+
> | Running: SQL/New_patches/2018-07-23-battery_manager_permissions.sql |
> +---------------------------------------------------------------------+
> | Running: SQL/New_patches/2018-07-23-battery_manager_permissions.sql |
> +---------------------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.01 sec)
>
> Query OK, 0 rows affected (0.00 sec)
> Records: 0  Duplicates: 0  Warnings: 0
>
> Query OK, 0 rows affected (0.00 sec)
> Records: 0  Duplicates: 0  Warnings: 0
>
> ERROR 1146 (42S02): Table 'IPMSA_LORIS.modules' doesn't exist
> +----------------------------------------------------------------+
> | Running: SQL/New_patches/2019-02-08-multiple_mri_protocols.sql |
> +----------------------------------------------------------------+
> | Running: SQL/New_patches/2019-02-08-multiple_mri_protocols.sql |
> +----------------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 0 rows affected (0.02 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 0 rows affected (0.02 sec)
>
> Query OK, 1 row affected (0.01 sec)
>
> Query OK, 0 rows affected (0.02 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 0 rows affected (0.03 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 0 rows affected (0.08 sec)
> Records: 0  Duplicates: 0  Warnings: 0
>
> Query OK, 9 rows affected (0.01 sec)
> Rows matched: 9  Changed: 9  Warnings: 0
>
> Query OK, 9 rows affected (0.09 sec)
> Records: 9  Duplicates: 0  Warnings: 0
>
> Query OK, 0 rows affected (0.05 sec)
> Records: 0  Duplicates: 0  Warnings: 0
>
> Query OK, 0 rows affected (0.00 sec)
> Rows matched: 0  Changed: 0  Warnings: 0
>
> Query OK, 0 rows affected (0.05 sec)
> Records: 0  Duplicates: 0  Warnings: 0
>
> Query OK, 0 rows affected (0.04 sec)
> Records: 0  Duplicates: 0  Warnings: 0
>
> Query OK, 0 rows affected (0.00 sec)
> Rows matched: 0  Changed: 0  Warnings: 0
>
> Query OK, 0 rows affected (0.07 sec)
> Records: 0  Duplicates: 0  Warnings: 0
>
> Query OK, 0 rows affected (0.06 sec)
> Records: 0  Duplicates: 0  Warnings: 0
>
> Query OK, 0 rows affected (0.00 sec)
> Rows matched: 0  Changed: 0  Warnings: 0
>
> Query OK, 0 rows affected (0.07 sec)
> Records: 0  Duplicates: 0  Warnings: 0
>
> +------------------------------------------------------------------+
> | Running: SQL/New_patches/2019-07-02-Add_Edit_DoB_Permissions.sql |
> +------------------------------------------------------------------+
> | Running: SQL/New_patches/2019-07-02-Add_Edit_DoB_Permissions.sql |
> +------------------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.01 sec)
>
> +---------------------------------------------------------+
> | Running: SQL/New_patches/2019-07-04-add_DoD_feature.sql |
> +---------------------------------------------------------+
> | Running: SQL/New_patches/2019-07-04-add_DoD_feature.sql |
> +---------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 0 rows affected (0.77 sec)
> Records: 0  Duplicates: 0  Warnings: 0
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.01 sec)
> Records: 1  Duplicates: 0  Warnings: 0
>
> Query OK, 1 row affected (0.00 sec)
> Records: 1  Duplicates: 0  Warnings: 0
>
> +--------------------------------------------------------------+
> | Running: SQL/New_patches/2019-07-05-Add_Language_feature.sql |
> +--------------------------------------------------------------+
> | Running: SQL/New_patches/2019-07-05-Add_Language_feature.sql |
> +--------------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 126974 rows affected (4.18 sec)
> Records: 126974  Duplicates: 0  Warnings: 0
>
>
> +--------------------------------------------------------------------------------+
> | Running:
> SQL/New_patches/2019-08-06-Add_date_display_format_config_setting.sql |
>
> +--------------------------------------------------------------------------------+
> | Running:
> SQL/New_patches/2019-08-06-Add_date_display_format_config_setting.sql |
>
> +--------------------------------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
> Records: 1  Duplicates: 0  Warnings: 0
>
> Query OK, 1 row affected (0.01 sec)
> Records: 1  Duplicates: 0  Warnings: 0
>
>
> +-------------------------------------------------------------------------------------------+
> | Running:
> SQL/New_patches/2019-10-09-move_MINCToolsPath_configuration_to_Config_tables.sql
> |
>
> +-------------------------------------------------------------------------------------------+
> | Running:
> SQL/New_patches/2019-10-09-move_MINCToolsPath_configuration_to_Config_tables.sql
> |
>
> +-------------------------------------------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
> Records: 1  Duplicates: 0  Warnings: 0
>
> Query OK, 1 row affected (0.00 sec)
> Records: 1  Duplicates: 0  Warnings: 0
>
> +-------------------------------------------------------------------------+
> | Running: SQL/New_patches/2019-10-29-adding_issues_attachments_table.sql |
> +-------------------------------------------------------------------------+
> | Running: SQL/New_patches/2019-10-29-adding_issues_attachments_table.sql |
> +-------------------------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 0 rows affected (0.03 sec)
>
> Query OK, 1 row affected (0.01 sec)
>
> Query OK, 1 row affected (0.00 sec)
> Records: 1  Duplicates: 0  Warnings: 0
>
> +---------------------------------------------------------+
> | Running: SQL/New_patches/2019-11-26-AddOtherSexEnum.sql |
> +---------------------------------------------------------+
> | Running: SQL/New_patches/2019-11-26-AddOtherSexEnum.sql |
> +---------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 0 rows affected (0.00 sec)
> Records: 0  Duplicates: 0  Warnings: 0
>
> Query OK, 0 rows affected (0.01 sec)
> Records: 0  Duplicates: 0  Warnings: 0
>
>
> +----------------------------------------------------------------------------+
> | Running:
> SQL/New_patches/2019-11-29-Add_upload_directory_configuration.sql |
>
> +----------------------------------------------------------------------------+
> | Running:
> SQL/New_patches/2019-11-29-Add_upload_directory_configuration.sql |
>
> +----------------------------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 1 row affected (0.01 sec)
> Records: 1  Duplicates: 0  Warnings: 0
>
> Query OK, 1 row affected (0.00 sec)
> Records: 1  Duplicates: 0  Warnings: 0
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
> Records: 1  Duplicates: 0  Warnings: 0
>
> Query OK, 1 row affected (0.01 sec)
> Records: 1  Duplicates: 0  Warnings: 0
>
> +--------------------------------------------------------+
> | Running: SQL/New_patches/2019-12-05-AddModuleTable.sql |
> +--------------------------------------------------------+
> | Running: SQL/New_patches/2019-12-05-AddModuleTable.sql |
> +--------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 0 rows affected (0.02 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.01 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.01 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.01 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.01 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.01 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.01 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.01 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.01 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.01 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> +-------------------------------------------------------+
> | Running: SQL/New_patches/2020-01-16-ModuleManager.sql |
> +-------------------------------------------------------+
> | Running: SQL/New_patches/2020-01-16-ModuleManager.sql |
> +-------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> ERROR 1048 (23000): Column 'userID' cannot be null
> ERROR 1048 (23000): Column 'userID' cannot be null
>
> +-------------------------------------------------------------------------------------------+
> | Running:
> SQL/New_patches/2020-01-20-adding_electrophysiology_browser_to_modules_table.sql
> |
>
> +-------------------------------------------------------------------------------------------+
> | Running:
> SQL/New_patches/2020-01-20-adding_electrophysiology_browser_to_modules_table.sql
> |
>
> +-------------------------------------------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> +------------------------------------------------------+
> | Running: SQL/New_patches/2020-02-18-MyPrefModule.sql |
> +------------------------------------------------------+
> | Running: SQL/New_patches/2020-02-18-MyPrefModule.sql |
> +------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> +----------------------------------------------------------------+
> | Running: SQL/New_patches/2020-02-24-CandidateProfileModule.sql |
> +----------------------------------------------------------------+
> | Running: SQL/New_patches/2020-02-24-CandidateProfileModule.sql |
> +----------------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> +----------------------------------------------------------------------+
> | Running: SQL/New_patches/2020-04-20-Rename_highlander_permission.sql |
> +----------------------------------------------------------------------+
> | Running: SQL/New_patches/2020-04-20-Rename_highlander_permission.sql |
> +----------------------------------------------------------------------+
> 1 row in set (0.01 sec)
>
> Query OK, 1 row affected (0.00 sec)
> Rows matched: 1  Changed: 1  Warnings: 0
>
>
> +---------------------------------------------------------------------------+
> | Running:
> SQL/New_patches/2020-04-27-AddViolatedScansOwnSitePermission.sql |
>
> +---------------------------------------------------------------------------+
> | Running:
> SQL/New_patches/2020-04-27-AddViolatedScansOwnSitePermission.sql |
>
> +---------------------------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 1 row affected (0.00 sec)
>
> ERROR 1048 (23000): Column 'userID' cannot be null
>
> +------------------------------------------------------------------------------+
> | Running:
> SQL/New_patches/2020-05-08-ChangeDefaultMPCGForMriViolationsLog.sql |
>
> +------------------------------------------------------------------------------+
> | Running:
> SQL/New_patches/2020-05-08-ChangeDefaultMPCGForMriViolationsLog.sql |
>
> +------------------------------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 0 rows affected (0.06 sec)
> Records: 0  Duplicates: 0  Warnings: 0
>
> +---------------------------------------------------------------+
> | Running: SQL/New_patches/2020-05-11-AddViolationsResolved.sql |
> +---------------------------------------------------------------+
> | Running: SQL/New_patches/2020-05-11-AddViolationsResolved.sql |
> +---------------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 0 rows affected (0.00 sec)
> Records: 0  Duplicates: 0  Warnings: 0
>
> +------------------------------------------------------------------------+
> | Running: SQL/New_patches/2020-05-15-RemoveObsoleteMriViolationsLog.sql |
> +------------------------------------------------------------------------+
> | Running: SQL/New_patches/2020-05-15-RemoveObsoleteMriViolationsLog.sql |
> +------------------------------------------------------------------------+
> 1 row in set (0.00 sec)
>
> Query OK, 0 rows affected (0.00 sec)
>
> Query OK, 0 rows affected (2.04 sec)
> Rows matched: 0  Changed: 0  Warnings: 0
>
> mysql> notee
>
> ===
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