[tools] Implement LorisInstance in tools directory

[CamilleBeau]

Describe the bug
Plenty of tools were failing because they had not been updated to pass a LorisInstance as an argument to various functions.

The following tools were failing:
delete_ignored_conflicts.php
detect_conflicts.php
lorisform_parser.php
lorisform_parser.php
score_instrument.php

To Reproduce
Steps to reproduce the behavior (attach screenshots if applicable):

1. Run the above tools as intended
2. See error

[CamilleBeau]

For some reason i'm not able to edit the description properly, but fix_candidate_age.php should also be on this list instead of lorisform_parser.php twice.

[driusan]

the critical ones were fixed, but there's still some other ones that need to be fixed according to @CamilleBeau.. @CamilleBeau can you give a list of which are outstanding?

[CamilleBeau]

the critical ones were fixed, but there's still some other ones that need to be fixed according to @CamilleBeau.. @CamilleBeau can you give a list of which are outstanding?

delete_ignored_conflicts.php
detect_conflicts.php

[CamilleBeau]

I believe this has been resolved for the 2 scripts above - I will test before EOD

[CamilleBeau]

Nevermind, still an issue for both:

(base) lorisadmin@cbeaudoin-dev:/var/www/loris/tools/data_integrity/data_deletion$ php delete_ignored_conflicts.php confirm
PHP Warning: Undefined variable $loris in /var/www/loris/tools/data_integrity/data_deletion/delete_ignored_conflicts.php on line 72
PHP Fatal error: Uncaught TypeError: NDB_BVL_Instrument::getDDEInstrumentNamesList(): Argument #1 ($loris) must be of type LORIS\LorisInstance, null given, called in /var/www/loris/tools/data_integrity/data_deletion/delete_ignored_conflicts.php on line 72 and defined in /var/www/loris/php/libraries/NDB_BVL_Instrument.class.inc:3253
Stack trace:
#0 /var/www/loris/tools/data_integrity/data_deletion/delete_ignored_conflicts.php(72): NDB_BVL_Instrument::getDDEInstrumentNamesList()
#1 {main}
thrown in /var/www/loris/php/libraries/NDB_BVL_Instrument.class.inc on line 3253

(base) lorisadmin@cbeaudoin-dev:/var/www/loris/tools$ php detect_conflicts.php -r all -y
Array
(
[r] => all
[y] =>
)
Removing ignored conflicts

PHP Fatal error: Uncaught TypeError: NDB_BVL_Instrument::factory(): Argument #1 ($loris) must be of type LORIS\LORISInstance, string given, called in /var/www/loris/tools/detect_conflicts.php on line 593 and defined in /var/www/loris/php/libraries/NDB_BVL_Instrument.class.inc:225
Stack trace:
#0 /var/www/loris/tools/detect_conflicts.php(593): NDB_BVL_Instrument::factory()
#1 /var/www/loris/tools/detect_conflicts.php(145): detectIgnoreColumns()
#2 {main}
thrown in /var/www/loris/php/libraries/NDB_BVL_Instrument.class.inc on line 225