[redcap/tools] ip_output_builder and redcap2linst terminal tag remove

[regisoc]

Brief summary of changes

• removes the {-@-} tag from redcap2linst tool so instruments will be created without it.
• adds a new ip_output_builder.php to generate ip_output.txt file for all instruments (LINST and PHP).
  • based on CBIG builder.
  • kept the parseElements() function from lorisform_parser.
  • added {-@-} tag at the end of each instrument parsing/copying.
  • added --add-linst option to add linst instrument in ip_output.txt.
  • added --add-meta option to prepend the linst corresponding .meta file in ip_output.txt when it exists.
  • added --one-instrument=INST option to only run the process on one instrument.
• deprecates lorisform_parser.sh in favour of ip_output_builder.php.

Documentation:

• Have you updated related documentation?

Testing instructions (if applicable)

1. Run tools/redcap2linst.php with REDCap instrument/API.
2. Run tools/ip_output_builder.php with the different arguments.
3. Check that other tools using the ip_output.txt file are successful.

Link(s) to related issue(s)

• Resolves [redcap] redcap2linst tool, generated LINST instrument terminal {-@-} crash #10663

[lapadulamichael]

I am also getting this error when trying to run tools/generate_tables_sql.php

PHP Fatal error:  Uncaught TypeError: preg_match(): Argument #2 ($subject) must be of type string, null given in /var/www/loris/tools/generate_tables_sql.php:43
Stack trace:
#0 /var/www/loris/tools/generate_tables_sql.php(43): preg_match()
#1 {main}
  thrown in /var/www/loris/tools/generate_tables_sql.php on line 43

and this one when trying to run tools/generate_tables_sql_and_testNames.php

Filename: /var/www/loris/tools/../project/tables_sql/aosi.sql
Filename: /var/www/loris/tools/../project/tables_sql/medical_history.sql
Filename: /var/www/loris/tools/../project/tables_sql/mri_parameter_form.sql
Filename: /var/www/loris/tools/../project/tables_sql/radiology_review.sql
PHP Warning:  Undefined array key 1 in /var/www/loris/tools/generate_tables_sql_and_testNames.php on line 38
PHP Fatal error:  Uncaught TypeError: preg_match(): Argument #2 ($subject) must be of type string, null given in /var/www/loris/tools/generate_tables_sql_and_testNames.php:38
Stack trace:
#0 /var/www/loris/tools/generate_tables_sql_and_testNames.php(38): preg_match()
#1 {main}
  thrown in /var/www/loris/tools/generate_tables_sql_and_testNames.php on line 38

[regisoc]

fixed.

[regisoc]

@lapadulamichael ready for another round.

[lapadulamichael]

@regisoc ip_output_builder.php and the scripts that use it seem to work perfectly fine.

Should we also update the documentation mentioning lorisform_parser here?

[regisoc]

@lapadulamichael nice catch, I might have forgotten the recursive flag in grep, thanks!

[lapadulamichael]

LGTM

[regisoc]

Updating assignee to @driusan for final review.

[MaximeBICMTL]

The REDCap part is minimal in that PR but looks fine to me. For the rest, I am not really familiar with that part of the codebase, especially the handling of non-JSON instruments, so trusting @lapadulamichael's and others review. No objection on my part.