CHANGELOG.md

CHANGELOG

• When adding content to this document, make sure to create a section for each module if the changes only impact a single module and that section does not already exist in the document. When changes affect the entire software, make sure to add them in the core section.

• When possible please provide the number of the pull request(s) containing the changes in the following format: PR #1234

LORIS 25.0 (Release Date: ????-??-??)

Core

Features

• Added new interface intended to be used for querying module data from PHP (PR #8215)
• Added the NOT NULL constraint on Project Name (PR #8295)

Updates and Improvements

• Rename subproject to Cohort (PR #7817)
• Create new CohortData and CohortController classes to use as data access model and transfer object (PR #7817)
• BVL Feedback widget only shows notifications for the users sites / projects (PR #7848)

Bug Fixes

• placeholder

Modules

ModuleName

• placeholder

EEG Browser

• Visualization:
  • Electrode 2D montage: detect if the coordinate space is in the ALS orientation to convert to RAS (nose up)
  • Use the optimal signal sampling that fulfills number of chunk displayed < MAX_VIEWED_CHUNKS
  • Fixes UI panels open/close glitches

Tools

• placeholder

Clean Up

• placeholder

Notes For Existing Projects

• placeholder

Notes For Developers

• placeholder

LORIS 24.1 (Release Date: 2022-10-05)

Core

Updates and Improvements

• Addition of PhaseEncodingDirection and EchoNumber columns to the mri_protocol and mri_protocol_violated_scans tables to allow for better discrimination between some MRI sequences.
• Addition of PhaseEncodingDirection and EchoNumber columns to the files, files_qcstatus and feedback_mri_comments tables to ensure uniqueness keys for specific GE sequences for which the SeriesUID/EchoTime combination is not enough (PR #8152).
• Addition of image_type, PhaseEncodingDirection and EchoNumber fields to the tables present in the "Could not identify scan" page of the MRI violation module (PR #8156)
• Modification of the list of headers displayed in the image panel headers table (PR #8157)

Bug Fixes

• Bug fix to the imaging uploader so that when clicking on an upload row, the row is highlighted and the proper log is being displayed in the log viewer (PR #8154)
• Remove SNR label from the image panel of the imaging browser when no SNR values can be found for the image (PR #8155)
• Add the missing download buttons for BVAL, BVEC and JSON files that comes with BIDS/NIfTI dataset/images. In addition, the "Download MINC" button has been renamed to a more generic label "Download Image" (PR #8159)
• Fix ConfigurationException bug (PR #8107)
• Fix PHP fatal error when running the LORIS installation script (PR #8108)
• Add psr/log to composer (PR #8109)
• Fixed broken DB calls in assign_missing_instruments and instruments (PR #8162)
• Add support for PHP 8.1 (PR #7989)

Modules

API

• Ability to use PSCID instead of the CandID in the candidates API (PR #8138)

LORIS 24.0 (Release Date: 2022-03-24)

Core

Features

• Data tables may now stream data as they're loading rather than waiting until all data has loaded. (PR #6853)
• Added support for Amazon S3 (PR #7963)
• Added ability for scripts to bulk load instrument data (PR #6869)
• New data dictionary framework and module (PR #6936)
• New classes to describe a data dictionary (PR #6938)

Updates and Improvements

• Module-specific permissions added for Survey Accounts, Imaging Behavioural Quality Control, and Behavioural Quality Control. (PR #6041)
• Addition of a new account_request_date in users table that will be used when requesting a new account and will be displayed in the User Accounts module (PR #6191)
• Candidate's age can be retrieved from the Candidate class in days, months, or years (PR #5945)
• Addition of autoSelect property to React SelectElement allows for auto-selection of only available select option (PR #6156)
• An AcquisitionDate field has been added to the files table (PR #6892)
• Field Data_entry_completion_status given its own column in flag, and renamed to Required_elements_completed (PR #6876)
• Addition of changeProject and resetProject helper functions to the LorisIntegrationTest class to help test project permissions (PR #6912)
• Unit tests added for the NDB_BVL_Instrument, NDB_Page, NDB_Factory, User, and UserPermissions libraries (PR #6819, PR #6804, PR #6776, PR #6765)
• The name of a Standard Date field in a LINST instrument must now end with the string _date. Otherwise, a LORIS exception is thrown. There is no restriction on the naming format of a Basic Date or MonthYear field. (PR #6923)
• React Form Select Element now has the ability to set an option in the element as a disabled option. (PR #7306)
• Pending accounts in Dashboard now includes DCC users (PR #7054)
• Cohort filter added to Behavioural QC module (PR #7430)
• Addition of date_format as a DataType in ConfigSettings (PR #6719)
• Addition of new tables to store PET HRRT data (PR #6142)
• Modification of the parameter_file table's Value field type to longtext (PR #7392)
• Addition of 4 configuration settings for the minc2bids converter (PR #7488)
• A PSR3 compatible logging interface was added (PR #7509)
• Multiple classes of errors flagged by phan are now fixed (multiple PRs)
• A LorisInstance class was added to represent an installed LORIS instance (PR #6118)
• Validation for DateElement (JS). (PR #7266)
• Session Current_stage default value changed for Not Started (PR #7102)
• Permissions were reorganized and categorized in the user accounts module (PR #7327)
• The EchoTime field has been added to the following tables: MRICandidateErrors, and mri_violations_log. EchoTime is necessary to distiguish MINC files for multi-echo aquisitions (PR #7515).
• The Center_name field in the mri_protocol table has been replaced by CenterID from the psc table. The default value of CenterID is NULL. Previously, the default for Center_name was AAAA or ZZZZ. (PR #7525)
• The statistics displayed in the dashboard was changed to only show the data relevant to the user's site(s). (PR #8132)

Bug Fixes

• A LINST instrument Date field name now appears correctly (not truncated) on the instrument if it includes the string _date. (PR #6923)
• A subtest with only static and/or static score fields (i.e. no values to submit) can be saved with no errors so that the instrument scoring script can be called. (PR #7124)
• When a superuser edits another user, the labels for each permission is correctly displayed (PR #7451)
• The imaging insertion pipeline (LORIS-MRI scripts) now starts automatically if you have the imaging uploader auto-launch set to true and your current upload overwrites an existing file (PR #7084).
• Script CouchDB_MRI_Importer now computes the correct names from the data dictionary entries associated to MRI comments (PR #7082).
• Candidate library now allows a null sex in the select() function to accommodate scanner candidates. This prevents an error from being thrown in the candidate parameters module. (PR #7058)
• Fix public pages with missing title (PR #7121)
• Fix "Go to main page" broken link (PR #7258)
• Download CSV fix to remove duplicates and entries that partially match the filtering criteria (PR #7242)
• Partially fix instrument escaping issues by reloading instrument and its data upon successful save (PR #7776)
• Fix recognition of null sessionID in NDB_BVL_Instrument (PR #8031)
• Fix delete_candidate.php / delete_timepoint.php failing because of json instruments / instruments with different table name than test_name (PR #8070)
• Fix bug where server_processes_manager had a timeout (PR #8071)
• Candidate profile page loads with only the visits listed that a user has access to if a candidate has some visits that the user should not see. Fixes error where page was not loading for this use case (PR #8072)

Modules

API

• Creation of a new version of the API under development (v0.0.4-dev) (PR #6944)
• Deletion of support for the oldest version of the API (v0.0.2) (PR #6944)
• Addition of a PATCH request for /candidates/$CandID/$VisitLabel to start next stage when the payload contains a "Visit" stage with "In Progress" as Status, when the current status of the Visit stage is "Not Started". (PR #7479)
• Handle characters that must be urlencoded (such as a space) in the API path for visit labels and projects. (PR #7478 & #7463)
• Markdown API documentation was moved into the module docs directory (PR #6151)

API Documentation (New Module)

• New module mostly intended for developers, this module provides a user interface to inspect and try LORIS modules API.

Behavioural QC

• Fix a fatal error if the datatable is filtered with "All instruments" (PR #6945)
• Fix for the Instrument filter to keep track of the selected value (PR #6945)

BrainBrowser

• Now uses Loris API to download imaging files (PR #7824)

Candidate Parameters

• Consents may now be grouped in UI of consent tab (PR #6042, PR #6044)
• Fix to prevent titles cut off (PR #6731)

Candidate Profile

• New integration test class to test project permissions (PR #6912)

Configuration

• Addition of configuration settings for the DICOM to BIDS insertion pipeline (PR #7937)
• Addition of configuration settings for the MINC to BIDS converter script (PR #7488)

Conflict Resolver

• Changes are now saved automatically, one by one. Once a conflict is resolved the cell that contains the input field will glow green. It is possible to change the resolved conflicts to a new value until the page is refreshed. (PR #7558)
• This module's API is now described in a Open API Specification file (schema.yml) that can be loaded in the new API Documentation module.
• Change the display of multi select values from "value1{@}value2" to "value1, value2" in the Correct Answer column of Unresolved and Resolved Conflicts. (PR #7239)

Create timepoint

• Fix a reindexing of the languages array which caused a database insert error. (PR #7145)
• Reorganization of the fields on the page to a more logical order, clean up of inefficient code and conditional display of select options based on previous selections (PR #7825)

Data Dictionary

• Changed instrument filter to multiselect (PR #7040)

DQT

• The dataquery module user interface has been completely redesigned. (PR #6908)

EEG Browser

• Signal Visualization, Events and Electrode map (PR #7387)
• Site/Project/cohort filters only displays entries user has permission for. (PR #7400)
• Addition of tables in the SQL schema, a filter on the main page of the module, and a download button on the session page to support new annotation features (PR #7345)
• New integration test class added to this module (PR #6922)

Genomic Browser

• CNV/CPG records added for candidates to view and test the CNV and Methylation tabs in the Genomic Browser (PR #6900)

Help Editor

• Cleaned up the deprecated column Parent Topic (PR #7025)

Imaging Uploader

• Fixed a bug that would prevent the imaging uploader from starting automatically even if you had the imaging uploader auto-launch set to true and your current upload overwrote an existing file (PR #7084)
• Use Loris API to view files (PR #7816)

Instrument Builder

• Fix for error 'Max value must be larger than min value' when clicking 'Add Row'. (PR #6810)

Instruments

• General help text added for instrument data entry (PR #6902)
• Fix to avoid select with required option in group fields to display as multiselect (PR #7254)
• Fixes to insert JSON instruments (PR #7155)

Issue Tracker

• Readability of comments and history was improved. (PR #6138)
• Update validation to allow NULL Site (For All Sites issues) (#6526)
• Fixing redirect and error reporting when creating a new issue (PR #7323)
• Show inactive users in the list of assignees as a disabled option. If the inactive user had already been previously assigned the issue, the disabled option appears but cannot be reselected. Inactive users can no longer be assigned new issues. (PR #7306)

Login

• Add option to toggle visibility on password input types. (PR #6210, #7043)

Media

• Fix to display the file name when editing a file (PR #7381)

Publication

• Display all filterable columns in datatable (#7277)
• Fix for file deletion (PR #7284)

User Accounts

• Fix a false positive validation error when a new LORIS user is added with "Make user name match email address" and "Generate new password". (PR #6803)
• Fix to allow a superuser to create new users with customizable permissions. (#6770)
• Indicate required fields (#6617)
• Fix to show superuser the labels of each permission when editing a user (PR #7451)

Tools

• Fix fatal errors in delete_candidate.php tool. (PR #6805, #7275)
• Fix fatal errors in fix_candidate_age.php (PR #7546)
• New tool generate_candidate_externalids.php to fill external IDs for all candidates where a NULL value is found. (PR #7095)
• New tool populate_visits.php to back-populate visits from the config.xml, session table and Visit_Windows table into the visit and visit_project_cohort_rel (#7663)
• Deprecation of the populate_visit_windows.php tool in favour of populate_visits.php (#7663)
• Fixes a bug in the way that the data dictionary entries associated to MRI comments were named in the CouchDB database (PR #7082).

Clean Up

• Removal of unused variables and unnecessary branching from getBattery() and getBatteryVerbose() functions (PR #7167)
• Removal of the violated_scans_edit permission (PR #6747)
• Removal for the need of the VisitLabel section of the config.xml file. All visit configurations and their association to projects are now in the database. The visits can be removed from the config.xml file after running the populate_visits.php script only. (#7663 & #7729)
• Removal of references to Reliability module in Raisinbread (PR #6895)
• Raisinbread visit stage inconsistency changed (PR #6896)
• HRRT patch sourced to Raisinbread (PR #6897)
• Improved consistency of RB data: field UploadLocation of table mri_upload now has an appropriate value (PR #7086)
• The default value of the ScannerID field of the mri_protocol table is now NULL instead of 0. This means that if a protocol is valid on all the study's scanners, then ScannerID of the protocol should be set to NULL (PR #7496)

Notes For Existing Projects

• The RegistrationProjectID column of the candidate table and the ProjectID column of the session table in the database are no longer nullable. This means that a value must be set in these fields BEFORE running the release SQL patch or it will fail.
• New function Candidate::getSubjectForMostRecentVisit replaces Utility::getCohortIDUsingCandID, adding the ability to determine which cohort a candidate belongs to given their most recent visit.
• LINST instrument class was modified to implement the getFullName() and getSubtestList() functions thus making entries in the test_names and instrument_subtests tables unnecessary for LINST instruments (PR #7169)
• The script tools/single_use/remove_publication_users_edit_perm_rel_duplicates.php should be run before upgrading LORIS.
• The Data_entry_completion_status column of instrument tables has been migrated to its own column in the flag table, and renamed to Required_elements_completed. After script Set_Required_elements_completed_flag.php is run, projects will need to delete the Data_entry_completion_status column of instrument tables. This can be accomplished by running Remove_Data_entry_completion_status_instr_column.php, and then sourcing the patch generated by this script. (PR #6876)
• If _setDataEntryCompletionStatus, _determineDataEntryCompletionStatus, and/or updateDataEntryCompletionStatus are called in any overrides, make sure to replace all instances with their newly named counterparts, _setRequiredElementsCompletedFlag, _determineRequiredElementsCompletedFlag, updateRequiredElementsCompletedFlag. (PR #6876)
• Deprecation of begintable and endtable elements in LINST instruments (PR #7183)
• Deletion of dateTimeFields and monthYearFields variables in instrument class. All references to these variables should be removed from project instruments. (PR #7183)
• Visit definitions is no longer done in the config.xml. An importer tool (populate_visits.php) is available to import the current setup into the visit table of the database. Make sure the visits displayed after these changes are what you expect. The visits can be removed from the config.xml file after the importer tool is run. (#7663 & #7729)
• There is a new abstract getDataDictionary() function in the instrument class for the new data dictionary framework. This is already implemented for LINST instruments, and existing instruments using LorisForm can use the \LorisFormDictionaryImpl trait to extract it in the same way as lorisform_parser.php did for the old datadict module.
• The name of a Standard Date field in a LINST instrument must now end with the string _date. Otherwise, a LORIS exception is thrown. There is no restriction on the naming format of a Basic Date or MonthYear field. (PR #6923)
• Run tools/single_use/Remove_duplicate_examiners.php to remove duplicate examiners that may have been created before bugfix. Make sure to run this script before running the SQL/New_patches/2021-09-28-Unique_examiners.sql. (PR #7462)
• Deletion of support for the oldest version of the API (v0.0.2) (PR #6944)
• Refer to instructions for clean up scripts meant to remove unused data in the SQL/Archive/24.0/Cleanup directory

Notes For Developers

• Eslint warnings cleanup (Various PRs)
• JQuery cleanup (Various PRs)
• PHPCS enabled for tools/ and test/ (Various PRs)
• Auto fix PHPCS (npm run lintfix:php) (#6825)

LORIS 23.0.0 (Release Date: 2020-06-12)

Core

Features

• Add configuration option to specify the format in which dates are displayed. (PR #5004)
• Configurable upload directory for data_release and document_repository modules (PR #5815)
• New radio components for forms. (PR #5846)

Updates and Improvements

• PHP minimum requirements raised to PHP 7.3 (PR #5723)
• Menus are now maintained by modules and no longer in the SQL database (PR #5839)
• New script created for streamlining instantiation of the Raisinbread demonstration database (PR #5260)
• New documentation for file permissions has been added to the README.md file. (PR #5323)
• Dashboard study progression section performance improvement (PR #5887)

Bug Fixes

• Fix edge-case that gave a confusing error message when changing password (PR #5956)
• Fix bug where examiner form field was incorrectly hidden (PR #6085)
• Fix special character double escaping in instruments (PR #6223)
• Fix duplicate examiners created / examiners overwritten (PR #7462)
• Prevent horizontal scroll on all modules (PR #6531)
• Fix to prevent help boxes to float over the page content when scrolling (PR #6721)

Modules

Candidate Profile

• New module created to provide dashboard of a single candidate's data across all modules. (Various PRs)

Issue Tracker

• The issue_tracker module now has the feature of uploading attachments to new or existing issues. (PR #5394)
• All sites now appear in the dropdown for site, not only study sites. (PR #6135)
• Status filter converted to a multiselect field. The Active Issues tab now displays Status filter: All except Closed. (PR #6529)
• Module filter fix to remove [object Object] entries. (PR #6522)
• Priority filter Low option added. (PR #6609)
• Fix to decode issue descriptions with special characters (&<>) (PR #6643)
• Add help text on Create/Edit Issue (PR #6600)

Battery Manager

• New module created to manage the entries in the test_battery table of the database. This allows projects to modify their instrument battery without requiring backend access. (PR #4221)

Module Manager

• New module created to manage the status of installed modules. (PR #6015)

Electrophysiology Browser

• New module created to view electrophysiology data within LORIS. (PR #5230)

Candidate Parameters

• Add tab to view and edit a candidate's date of birth. (PR #4915)
• Add date of death feature for LORIS. Store and calculate age based on a date of death for candidates. (PR #4929)

Create Timepoint

• Add language parameter when creating a new timepoint for multilingual studies. (PR #4976)

Data Release

• Add filters to data release module. (PR #5224)

MRI Violations

• Add support for multiple MRI protocols (PR #4321)

Login

• Pwd Expiry: Password validation for rejection if matching user's email or username or not matching password confirmation. (PR #6615, #6705, #6611)

Statistics

• Fix to prevent Notice error logs (PR #6720)
• Projects filter only displays projects user has permission for. (PR #6706)

Genomic Browser

• In Profile and SNP screens, display cohort title instead of id. (PR #6633)

Survey

• Fix Notice error logs and infinite redirect. (PR #6644)

User Accounts

• Fix typo in user_accounts_multisite permission name. (PR #6656)

DQT

• Improve the visibility of some dropdown elements (PR #6602)

Clean Up

• New tool for detection of multiple first visits for a candidate (prevents a database exception). It is recommended to run this tool for existing projects (PR #5270)
• Heroku postdeploy script cleanup (PR #5275)
• Vagrantfile Deprecation (PR #5319)
• The data_integrity_flag module was removed. (PR #5824)

Notes For Existing Projects

• PHP should be upgraded to 7.3 to before upgrading LORIS.
• For dev instances, php7.3-curl is now a required dependency.
• Legacy Quickform instruments may have issues due to code changes (PR #4928)
• Customized entries in the LorisMenu and LorisMenuPermissions tables need to be transferred to the new module table and handled accordingly. (PR #5839)
• Change of name from quatUser and quatPassword to adminUser and adminPassword (PR #5785)
• The data_integrity_flag module was removed. Projects still using the module should copy the code into the override directory and re-add the necessary SQL to add it to the list of modules.(PR #5824)
• New tool for detection of multiple first visits for a candidate (prevents a database exception). It is recommended to run this tool for existing projects (PR #5270)
• New tool for automatically adding modules to the modules table. This tool should be used by projects having custom modules not in LORIS. (PR #5913)
• Duplicate filenames in the data release module will cause an error when downloading. Make sure to remove all filename duplications before upgrading to this version. (PR #6461)
• New tool for detecting and reporting the presence of double escaped special characters in the database instruments (PR #6477)
• Run tools/single_use/Remove_duplicate_examiners.php to remove duplicate examiners that may have been created before bugfix. Make sure to run this script before running the SQL/New_patches/2021-09-28-Unique_examiners.sql. (PR #7462)

Notes For Developers

• The tool phpstan has been added to our automated test suite. (PR #4928)
• Config files for static analysis have been moved to the test/ directory. (PR #5871)
• Dashboard was refactored to turn panels into module widgets. (PR #5896)
• Add CSSGrid component type (PR #6090)
• React Form Select Element now has the ability to set an option in the element as a disabled option. (PR #7306)