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

[Shen Wang]

Hi Alfredo,

It seems like you have an issue with the user_perm_rel table.
I need more information to debug this issue.
Could you send me the data in the table (22.0.4)?

Thanks.
Best regards
Shen


On Fri, 15 Jan 2021 at 21:38, 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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>


-- 
Shen Wang
Loris <https://github.com/aces/Loris>  Developer
Montreal Neurological Institute
McGill University
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