[tools] Tool failures

[skarya22]

Brief summary of changes

• These tools had multiple broken parts. Mostly related to CandidateID changes, but also others

Closes #9629
Closes #9631
Closes #9633

Testing instructions (if applicable)

1. Try running the scripts

[driusan]

@jeffersoncasimir these seem to be mostly the CandID changes (with 1 or 2 lorisInstance ones).

Can you review?

[driusan]

@skarya22 PHPCS is failing.

FILE: /home/runner/work/Loris/Loris/tools/detect_conflicts.php
--------------------------------------------------------------------------------
FOUND 3 ERRORS AFFECTING 3 LINES
--------------------------------------------------------------------------------
 573 | ERROR | Doc comment for parameter "$lorisInstance" missing
 577 | ERROR | Doc comment for parameter $instruments does not match actual
     |       | variable name $lorisInstance
 578 | ERROR | Doc comment for parameter $confirm does not match actual
     |       | variable name $instruments
--------------------------------------------------------------------------------

[jeffersoncasimir]

@skarya22 This PR appears to be based on 26.0-release instead of main. Not necessarily problematic but may not accurately reflect the state to be tested

[jeffersoncasimir]

Unfortunately, none of these errors seem caused by these changes, but this PR is shining a light on many existing issues.

All scripts were tested with valid inputs with each of their different forks (ex: tosql, confirm). They were not tested with "invalid inputs" (ex: non-existing IDs). Non-mentions can be assumed to be tested and functional (no fatal errors).

I ran tools/data_integrity/data_deletion/delete_candidate.php with confirm and got the following error:

Dropping all DB entries for candidate CandID: 648507 And PSCID: DRV0005
PHP Fatal error:  Uncaught PDOException: SQLSTATE[23000]: Integrity constraint violation: 1451 Cannot delete or update a parent row: a foreign key constraint fails (`jcasimir_test_26`.`dataquery_run_results`, CONSTRAINT `dataquery_run_results_ibfk_1` FOREIGN KEY (`CandidateID`) REFERENCES `candidate` (`ID`)) in /var/www/Loris/php/libraries/Database.class.inc:630
Stack trace:
#0 /var/www/Loris/php/libraries/Database.class.inc(630): PDO->exec()
#1 /var/www/Loris/tools/data_integrity/data_deletion/delete_candidate.php(367): Database->delete()
#2 /var/www/Loris/tools/data_integrity/data_deletion/delete_candidate.php(118): deleteCandidate()
#3 {main}
  thrown in /var/www/Loris/php/libraries/Database.class.inc on line 630

I ran tools/data_integrity/data_deletion/delete_timepoint.php with tosql and got the following error:

PHP Fatal error:  Uncaught TypeError: fwrite(): Argument #1 ($stream) must be of type resource, bool given in /var/www/Loris/tools/data_integrity/data_deletion/delete_timepoint.php:503
Stack trace:
#0 /var/www/Loris/tools/data_integrity/data_deletion/delete_timepoint.php(503): fwrite()
#1 /var/www/Loris/tools/data_integrity/data_deletion/delete_timepoint.php(460): _exportSQL()
#2 /var/www/Loris/tools/data_integrity/data_deletion/delete_timepoint.php(120): deleteTimepoint()
#3 {main}
  thrown in /var/www/Loris/tools/data_integrity/data_deletion/delete_timepoint.php on line 503

I ran tools/data_integrity/data_deletion/delete_timepoint.php with confirm and got the following error:

PHP Fatal error:  Uncaught PDOException: SQLSTATE[23000]: Integrity constraint violation: 1451 Cannot delete or update a parent row: a foreign key constraint fails (`jcasimir_test_26`.`physiological_file`, CONSTRAINT `FK_session_ID` FOREIGN KEY (`SessionID`) REFERENCES `session` (`ID`)) in /var/www/Loris/php/libraries/Database.class.inc:630
Stack trace:
#0 /var/www/Loris/php/libraries/Database.class.inc(630): PDO->exec()
#1 /var/www/Loris/tools/data_integrity/data_deletion/delete_timepoint.php(365): Database->delete()
#2 /var/www/Loris/tools/data_integrity/data_deletion/delete_timepoint.php(120): deleteTimepoint()
#3 {main}
  thrown in /var/www/Loris/php/libraries/Database.class.inc on line 630

tools/detect_conflicts.php has this error, when used with -i:

PHP Fatal error:  Uncaught TypeError: getCurrentUnresolvedConflicts(): Return value must be of type array, LORIS\Database\Query returned in /var/www/Loris/tools/detect_conflicts.php:358
Stack trace:
#0 /var/www/Loris/tools/detect_conflicts.php(190): getCurrentUnresolvedConflicts()
#1 {main}
  thrown in /var/www/Loris/tools/detect_conflicts.php on line 358

detect_duplicated_commentids.php has an error, similar to the previous:

PHP Fatal error:  Uncaught Error: Cannot use object of type LORIS\Database\Query as array in /var/www/Loris/tools/detect_duplicated_commentids.php:199
Stack trace:
#0 /var/www/Loris/tools/detect_duplicated_commentids.php(127): getCommentIDs()
#1 {main}
  thrown in /var/www/Loris/tools/detect_duplicated_commentids.php on line 199

Not sure what to make of this: php fix_timepoint_date_problems.php add_instrument 300001 1 aosi

Error: failed to add the instrument aosi for timepoint (1):
Error: Database user named lorisadmin does not exist. Please create and then retry script

I otherwise approve of the code changes.

[skarya22]

@jeffersoncasimir Thank you for catching those! Resolved them

[jeffersoncasimir]

I ran tools/data_integrity/data_deletion/delete_candidate.php with tosql and got the following error:

PHP Fatal error:  Uncaught TypeError: preg_match_all(): Argument #2 ($subject) must be of type string, array given in /var/www/Loris/tools/data_integrity/data_deletion/delete_candidate.php:201

I ran tools/data_integrity/data_deletion/delete_candidate.php with confirm and got the following error:

PHP Fatal error:  Uncaught PDOException: SQLSTATE[23000]: Integrity constraint violation: 1451 Cannot delete or update a parent row: a foreign key constraint fails (`jcasimir_test_26`.`physiological_event_file`, CONSTRAINT `FK_physio_file_ID` FOREIGN KEY (`PhysiologicalFileID`) REFERENCES `physiological_file` (`PhysiologicalFileID`)) in /var/www/Loris/php/libraries/Database.class.inc:630

I ran tools/data_integrity/data_deletion/delete_timepoint.php with confirm and got the following error (same as delete_candidate right above -- tosql is now functional):

PHP Fatal error:  Uncaught PDOException: SQLSTATE[23000]: Integrity constraint violation: 1451 Cannot delete or update a parent row: a foreign key constraint fails (`jcasimir_test_26`.`physiological_event_file`, CONSTRAINT `FK_physio_file_ID` FOREIGN KEY (`PhysiologicalFileID`) REFERENCES `physiological_file` (`PhysiologicalFileID`)) in /var/www/Loris/php/libraries/Database.class.inc:630

I am struggling to test tools/detect_conflicts.php in a meaningful way. The previous error is gone, but I can't get it to work with any instrument; it always results in: the instrument is not set or there are no commentids. When I do -i all it will fail at this error that will be addressed by another PR:

PHP Fatal error:  Uncaught OutOfBoundsException: Invalid field Examiner for instrument bmi in /var/www/Loris/php/libraries/NDB_BVL_Instrument.class.inc:1412

I ran tools/detect_duplicated_commentids.php and got the following error:

PHP Fatal error:  Uncaught DomainException: Attempt to use pselectRow on a query that returns multiple rows in /var/www/Loris/php/libraries/Database.class.inc:848

tools/fix_timepoint_date_problems.php appears to work as expected!