[Tools] Enable PHPCS for fix_timepoint_date_problems.php

[laemtl]

Replaces #5984

This PR also makes changes to the User and Timepoint class, to fix return type inaccuracies.

To test

• checkout the branch
• run PHPCS and check that there is no errors:
  npm run lint:php
• run the tool and check that there is no errors:
  php tools/fix_timepoint_date_problems.php

[jesscall]

Hi @laemtl!

I was wondering if you could provide some information on how this could be tested?

Thanks!

[jesscall]

Hi @laemtl!
Here are some suggested improvements:

1. Check that args are set
2. When using diagnose, I am getting an error telling me it cannot diagnose a non-started timepoint even though the visits have been started.

$ php fix_timepoint_date_problems.php diagnose 676061
Candidate: 676061 

 Timepoint V1 ; SubProjectID: 2 ; Effective DOB: 1980-02-02 ; (SessionID): 2145 
Error: failed to get the list of needed instruments for candidate (676061), timepoint (2145):
Error: Cannot diagnose the non-started timepoint (2145) for candidate (676061)!

 Timepoint V2 ; SubProjectID: 1 ; Effective DOB: 1980-02-02 ; (SessionID): 2147 
Error: failed to get the list of needed instruments for candidate (676061), timepoint (2147):
Error: Cannot diagnose the non-started timepoint (2147) for candidate (676061)!

 Timepoint V3 ; SubProjectID: 2 ; Effective DOB: 1980-02-02 ; (SessionID): 2148 
Error: failed to get the list of needed instruments for candidate (676061), timepoint (2148):
Error: Cannot diagnose the non-started timepoint (2148) for candidate (676061)!

 Timepoint V4 ; SubProjectID: 3 ; Effective DOB: 1980-02-02 ; (SessionID): 2149 
Error: failed to get the list of needed instruments for candidate (676061), timepoint (2149):
Error: Cannot diagnose the non-started timepoint (2149) for candidate (676061)!

 Timepoint V5 ; SubProjectID: 3 ; Effective DOB: 1980-02-02 ; (SessionID): 2150 
Error: failed to get the list of needed instruments for candidate (676061), timepoint (2150):
Error: Cannot diagnose the non-started timepoint (2150) for candidate (676061)!

 Timepoint V6 ; SubProjectID: 3 ; Effective DOB: 1980-02-02 ; (SessionID): 2151 
Error: failed to get the list of needed instruments for candidate (676061), timepoint (2151):
Error: Cannot diagnose the non-started timepoint (2151) for candidate (676061)!

3. fix_date option returns an error (on dob and on visit)

$ php fix_timepoint_date_problems.php fix_date 676061 2020-01-01 dob
PHP Notice:  Undefined index: UserID in /var/www/loris/php/libraries/User.class.inc on line 256
PHP Fatal error:  Uncaught TypeError: Return value of User::getUsername() must be of the type string, null returned in /var/www/loris/php/libraries/User.class.inc:256
Stack trace:
#0 /var/www/loris/tools/fix_timepoint_date_problems.php(415): User->getUsername()
#1 /var/www/loris/tools/fix_timepoint_date_problems.php(222): fixDate(Object(LORIS\StudyEntities\Candidate\CandID), 'dob', '2020-01-01')
#2 {main}
  thrown in /var/www/loris/php/libraries/User.class.inc on line 256

$ php fix_timepoint_date_problems.php fix_date 676061 2020-01-01 V1 2145
PHP Notice:  Undefined index: UserID in /var/www/loris/php/libraries/User.class.inc on line 256
PHP Fatal error:  Uncaught TypeError: Return value of User::getUsername() must be of the type string, null returned in /var/www/loris/php/libraries/User.class.inc:256
Stack trace:
#0 /var/www/loris/tools/fix_timepoint_date_problems.php(415): User->getUsername()
#1 /var/www/loris/tools/fix_timepoint_date_problems.php(222): fixDate(Object(LORIS\StudyEntities\Candidate\CandID), 'v1', '2020-01-01')
#2 {main}
  thrown in /var/www/loris/php/libraries/User.class.inc on line 256

[jesscall]

Exit script after displaying help message if args are missing. Also check that argv[2], [3]..etc are set, otherwise:

PHP Notice:  Undefined offset: 1 in /var/www/loris/tools/fix_timepoint_date_problems.php on line 92
PHP Notice:  Undefined offset: 2 in /var/www/loris/tools/fix_timepoint_date_problems.php on line 95
PHP Fatal error:  Uncaught TypeError: Argument 1 passed to LORIS\StudyEntities\Candidate\ValidatableIdentifier::__construct() must be of the type string, null given, called in /var/www/loris/tools/fix_timepoint_date_problems.php on line 95 and defined in /var/www/loris/src/StudyEntities/Candidate/ValidatableIdentifier.php:58
Stack trace:
#0 /var/www/loris/tools/fix_timepoint_date_problems.php(95): LORIS\StudyEntities\Candidate\ValidatableIdentifier->__construct(NULL)
#1 {main}
  thrown in /var/www/loris/src/StudyEntities/Candidate/ValidatableIdentifier.php on line 58

[laemtl]

Thank you @jesscall for all you suggestions. I will have a look shortly.

[laemtl]

@jesscall You were right, there were several problems in this script, thanks to have reported them. I made an attempt to fix them, let me know what you think.
@driusan, @ridz1208 I would like to know if there is a better approach to what has been done L377. I wonder if it may be not convenient to have a Loris user matching your session user.

[laemtl]

@driusan What is missing in this PR to be ready?

[driusan]

The change to the timepoint class still needs to be reverted.

[laemtl]

@driusan Done! I opened an issue for discussion: #7282

[laemtl]

Blocked by #6825

[driusan]

#6825 is merged

[laemtl]

@driusan Ready to be reviewed/merged.

[laemtl]

@driusan Rebased.

[driusan]

@jesscall GitHub says you requested changes.. can you update your review so I can merge (if you're satisfied..)?