[tools] Implement lorisInstance in tools directory

[victori444]

Brief summary of changes

• Implements lorisInstance in detect_conflicts.php

Testing instructions (if applicable)

1. Run detect_conflicts.php and verify that no errors are thrown and that it functions as intended

Link(s) to related issue(s)

• Resolves [tools] Implement LorisInstance in tools directory #8058 (Reference the issue this fixes, if any.)

[CamilleBeau]

@victori444 Assigning to you to resolve conflicts and then I'll test / review!

[driusan]

does this resolve the issue listed or only partially resolve it? (There are many places listed in the issue and merging it with "Resolved" will close the issue automatically)

[CamilleBeau]

According to the comments of the issue, these were the only 2 remaining out of the initial list

[CamilleBeau]

I'm getting a lot of these when running detect_conflicts -r all -y:

[CamilleBeau]

Getting this error when running:

(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 Error: Cannot use object of type LORIS\Database\Query as array in /var/www/loris/tools/detect_conflicts.php:595
Stack trace:
#0 /var/www/loris/tools/detect_conflicts.php(146): detectIgnoreColumns()
#1 {main}
thrown in /var/www/loris/tools/detect_conflicts.php on line 595

[victori444]

Getting this error when running:

(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 Error: Cannot use object of type LORIS\Database\Query as array in /var/www/loris/tools/detect_conflicts.php:595
Stack trace:
#0 /var/www/loris/tools/detect_conflicts.php(146): detectIgnoreColumns()
#1 {main}
thrown in /var/www/loris/tools/detect_conflicts.php on line 595

Hm I don't get this error - I think this may be the error that the PR changes resolve since line 595 in the current script is where $commentids is being accessed as an array ($commentids[0]['CommentID'])

[CamilleBeau]

Printing a bunch of blank lines when running this - can you check to see if that's happening for you also?

[CamilleBeau]

Gave this another test, it looks like the script is not compatible for linst instruments.

It also seems as thought here may be an issue with detecting the conflicts - I created a conflict (participant MTL008 in raisinbread, radiology review in timepoint V1) and nothing was printed out in the script

[victori444]

Fixed on my end (not pushed yet) to work for linst instruments & properly detect ignored conflicts - this is to be revisited as the script may need to be optimized for memory usage

[driusan]

If there are fixes needed for memory usage that sounds like a different issue. Is this ready to merge?