Refactor mri_protocol into scan_type_identification with similar structure as mri_protocol_checks

[cmadjar]

Brief summary of changes

This is the LORIS side changes required for the refactoring of the mri_protocol table to be like mri_protocol_checks. During an imaging call, it was suggested by @driusan to rename the table to scan_type_identification to make it clear that the table is used for scan type identification which will avoid future confusion with the mri_protocol_checks table which validates the protocol of the scan used against some parameters.

Note: because of this naming changes, the mri_protocol_group, mri_protocol_group_target and mri_protocol_violated_scans were renamed to scan_type_identification_group, scan_type_identification_group_target and scan_type_identification_failure to remain consistent and avoid more confusion when looking at the tables.

List of changes:

• [x] modified default schema
• [x] created a patch that adds the scan_type_identification and scan_type_identification_failures tables and alters the mri_protocol_group and mri_protocol_group_target tables
• [x] addition of two scripts that
  • [x] populate the new scan_type_identification table based on the content of mri_protocol
  • [x] populate the new scan_type_identification_failures table based on the content of mri_protocol_violated_scans
• [x] created a cleanup patch to remove the old mri_protocol table
• [x] documented the update process in CHANGELOG under Notes for existing projects + in the description of the PR
• [x] modified the MRI violation module where the protocol is displayed (that is going to be fun, LOL)
• [x] updated raisinbread with SQL changes
• [x] checked if those changes affect the API, if so, modify the API code -> no change needed
• [x] checked whether tests need to be updated -> no change needed
• [ ] modify the LORIS-MRI code to use the new table

Testing instructions (if applicable)

1. test that the default schema can be sourced
2. test the patch 2022-05-17-add-scan_type_identification-table-refactor-mri_protocol-part-1.sql
3. run the PHP tool script that populates the scan_type_identification table based on the content of mri_protocol
4. test the MRI violations module

Notes for existing projects

mri_protocol, mri_protocol_group, mri_protocol_group_target and mri_protocol_violated_scans have been redesigned and renamed to scan_type_parameter, scan_type_parameter_group, scan_type_parameter_group_target and scan_type_identification_failure respectively. To upgrade to the new structure, follow the following steps:

1. run SQL patch SQL/New_patches/2022-05-17-add-scan_type_identification-table-refactor-mri_protocol-part-1.sql
2. run tools/single_use/populate_scan_type_parameter_table_based_on_mri_protocol_table.php to populate scan_type_parameter based on the entries present in mri_protocol
3. run tools/single_use/populate_scan_type_identification_failure_table_based_on_mri_protocol_violated_scans_table.php to populate scan_type_identification_failure based on the entries present in mri_protocol_violated_scans
4. optionally, run the two SQL clean up patches to remove mri_protocol and mri_protocol_violated_scans after ensuring there are proper backups of those tables. (Clean up patches are: SQL/Cleanup_patches/2022-05-17-remove-mri_protocol.sql and SQL/Cleanup_patches/2022-05-17-remove-mri_protocol_violated_scans.sql)

Link(s) to related issue(s)

• Related to https://github.com/aces/Loris-MRI/issues/363

[cmadjar]

@driusan @nicolasbrossard before I move forward with this work, could you take a look at the new SQL structure and let me know if the changes make sense? I'd like to validate the SQL changes before changing the code everywhere, including the LORIS-MRI side.

Thank you!

[cmadjar]

@driusan thank you for the review!! See my answers to your comments. Let me know your thoughts. We can also discuss during the imaging call. Thanks!

[cmadjar]

@driusan ready for another round of review. All your comments have been replied to or taken care of in the last few commits. I also fixed the dashboard automated tests in theory.

Thank you!

[cmadjar]

@driusan @kongtiaowang I don't understand where the error comes from in the tests. Would you mind taking a look?