LORIS scripts in the tools directory - aces/Loris GitHub Wiki

HOME > SETUP > LORIS SCRIPTS IN THE TOOLS/ DIRECTORY

• assign_missing_instruments.php
• config_to_db.php [DEPRECATED]
• delete_candidate.php
• detect_conflicts.php
• fix_timepoint_date_problems.php
• generate_tables_sql.php
• populate_visit_windows.php
• quickform_parser.php
• score_instrument.php

This section is under construction.

Note: scripts may generate PHP Notice messages, which is normal and should not affect output.

See Also: CouchDB* loading scripts -> Loading the Data Querying Tool

Adds instruments to test battery for candidates after timepoints have already been started and populated. By default this script will only print (but not add) instruments detected missing from candidate timepoints according to the current test battery definitions. Add the command-line argument “confirm” to populate these missing instruments in the database.

This script was introduced in a previous version of LORIS (14.10) as we migrated much of the LORIS configuration from the config.xml file to the MySQL database. This script can be used by projects who are running an old version of LORIS and who have not yet updated to the new configuration module. See the readme in the configuration module for more information.

This script deletes all DB table entries for one candidate.

To run:

// substitute DCCID and PSCID with the IDs of the candidate you wish to delete

php delete_candidate DCCID PSCID

General description: Detects double data entry conflicts missing from the conflicts_unresolved database table.

Usage:

• Detect conflicts for a specific instrument:
  php detect_conflicts.php -i InstrumentName
• Detect conflicts for a specific instrument and visit/timepoint:
  php detect_conflicts.php -i InstrumentName -t Timepoint
• Detect conflicts for a all instrument:
  php detect_conflicts.php -i all
• Detect and insert conflicts into conflicts_unresovled table: use flag -c
  php detect_conflicts.php -c -i InstrumentName
• To update (remove and re-insert) conflicts into conflicts_unresovled table: use flag -m
  php detect_conflicts.php -m -i InstrumentName

General description: This script diagnoses and corrects the date problems in a candidate's profile and adds missing instruments to the behavioural battery. It can also be used to adds an instrument for a candidate, for a specific visit.

The procedure to correct the problems is:

• run script with command-line argument fix_date to UPDATE the date fields in the candidate/session table (as needed)
• run script with command-line argument diagnose to get the difference in batteries
• run script with command-line argument add_instrument to add missing instruments, and create new feedback

Ways to use this script:

• to get a help screen run: php fix_timepoint_date_problems.php help
• to fix dates (when fixing stage dates, sessionID must be specified)
  • php fix_timepoint_date_problems.php diagnose <candID> [<sessionID>]
  • php fix_timepoint_date_problems.php diagnose <candID> [<newCorrectDate> <dob/edc/>]
  • php fix_timepoint_date_problems.php diagnose <candID> [<sessionID> <newCorrectDate> <screening/visit>]
• to fix behavioural battery (run only once the dates are fixed). This adds an instrument to a candidate's visit/session.
  • php fix_timepoint_date_problems.php add_instrument <candID> <sessionID> <test_name>

This script takes the ip_output.txt file generated from quickform_parser.php and outputs an sql build file for the table of each instrument it finds in the ip_output.txt file. These sql files are output to the tables_sql/ subdirectory.

To run:

php generate_tables_sql.php

This script populates the Visit_Windows table based on the config.xml. This should usually be run on a one time basis, and then the Visit_Windows table should be kept up to date manually, though the script will only insert new visits, so it can be run multiple times if need be.

The Visit_Windows table should be kept up to date so that places that don't have access to the config.xml (ie. the MRI pipeline scripts) can still check if a visit is valid. It's also used by the Utility::getVisits utility function in PHP, so if the table is not up to date some drop downs may not appear correctly.

To run:

php populate_visit_windows.php

This parses all of the instruments and generates a staging file (ip_output.txt) which can be used by data_dictionary_builder.php and generate_tables_sql.php. You can also run the script for a single instrument at a time.

To run:

// For all instruments:

find ../project/instruments/ | php quickform_parser.php

// For a single instrument (replace INSTRUMENTFILE with the correct filename):

find ../project/instruments/INSTRUMENTFILE | php quickform_parser.php

This tools scores any registered instrument that was built using the NDB_BVL_Instrument class and that has a working score() method. It can be used to score all sessions of a given instrument, or one specific instrument for one candidate, at one session.

To score all instances of an instrument again:

The 'all' argument scores all records of an instrument that belong to an active timepoint and whose data entry is completed and administration is not 'None'.

To run:

// replace <test_name> with the instrument you would like to score

score_instrument.php <test_name> all

The non-administered records' scores have to be reset in the DB - this tool does not manage them

To score for a single candidate:

// replace <test_name> with the instrument you would like to score
// replace <candID> with the ID of the candidate
// replace <sessionID> with the ID of the session

score_instrument.php <test_name> one <candID> <sessionID>