LORIS Release v25.0.0

[driusan]

What's Changed

• [EEG] Database Architecture for HED Tags by @jesscall in [EEG] Database Architecture for HED Tags #8036
• [dashboard][Study Progression] Add tooltip visualising of Total in line chart by @satvik-tha-god in [dashboard][Study Progression] Add tooltip visualising of Total in line chart #8123
• [candidate_list] Remove meaningless Latest_Visit_Status column by @driusan in [candidate_list] Remove meaningless Latest_Visit_Status column #7759
• [publication] Add columns to publications by @pierre-p-s in [publication] Add columns to publications #7361
• [Core] Remove duplicated getActiveModules function by @driusan in [Core] Remove duplicated getActiveModules function #7446
• [Form.js] No required min/max for numeric elements by @driusan in [Form.js] No required min/max for numeric elements #8197
• [new_profile] Use API for candidate creation and swal for success by @driusan in [new_profile] Use API for candidate creation and swal for success #7755
• [EEG Browser] Add ability to view annotations in event panel and overlaid on signal viewer by @laemtl in [EEG Browser] Add ability to view annotations in event panel and overlaid on signal viewer #8235
• [login] Add code sanitizer before dangerouslySetInnerHTML by @CamilleBeau in [login] Add code sanitizer before dangerouslySetInnerHTML #7491
• [EEG Browser] Annotations: Add new and HED tags by @laemtl in [EEG Browser] Annotations: Add new and HED tags #8236
• [dashboard] Use user site permissions for dashboard charts by @CamilleBeau in [dashboard] Use user site permissions for dashboard charts #8132
• QueryEngine interface by @driusan in QueryEngine interface #8215
• [DB schema] UNIQUE Project name by @xlecours in [DB schema] UNIQUE Project name #8243
• [instrument_builder] ADDED: field warnings for maximum length in Instrument Builder module by @satvik-tha-god in [instrument_builder] ADDED: field warnings for maximum length in Instrument Builder module #8112
• Add PHP 8.2 support, drop 8.0 support by @driusan in Add PHP 8.2 support to main branch, drop 8.0 support #8264
• [bvl_feedback][dashboard] Add project/site specs to widget by @CamilleBeau in [bvl_feedback][dashboard] Add project/site specs to widget #7848
• [Core] Allow parallel handling of requests from same session by @driusan in [Core] Allow parallel handling of requests from same session #7445
• [LorisInstance] add getModule function by @driusan in [LorisInstance] add getModule function #8221
• [dataquery] Define new swagger schema for data query API by @driusan in [dataquery] Define new swagger schema for data query API #8219
• [new_timepoint] only show null language option when multiple exist by @CamilleBeau in [new_timepoint] only show null language option when multiple exist #8253
• Add CITATION.cff file by @driusan in Add CITATION.cff file #7513
• [candidate_parameters] Add date restriction for consent withdrawal by @zaliqarosli in [candidate_parameters] Add date restriction for consent withdrawal #8298
• [Modules] Replace Module->getDataDictionary with Module QueryEngine dictionary. by @driusan in [Modules] Replace Module->getDataDictionary with Module QueryEngine dictionary. #8260
• [survey_accounts] Clean up after Email col removed by @zaliqarosli in [survey_accounts] Clean up after Email col removed #8313
• [mri_violations] Convert module to React and update UI by @driusan in [mri_violations] Convert module to React and update UI #7473
• [Instrument] Remove exception from NDB_BVL_Instrument::factory by @driusan in [Instrument] Remove exception from NDB_BVL_Instrument::factory #8290
• [core] Remove \Module::factory, update remaining instances to $loris->getModule() by @driusan in [core] Remove \Module::factory, update remaining instances to $loris->getModule() #8287
• [Core] Remove Database::singleton function by @driusan in [Core] Remove Database::singleton function #8427
• Make the number of days since last login before making a user inactive a config by @cmadjar in Make the number of days since last login before making a user inactive a config #8416
• [instruments] Display Candidate Age at Death if postMortem is true by @zaliqarosli in [instruments] Display Candidate Age at Death if postMortem is true #8362
• [session] Add date of status change to session table by @CamilleBeau in [session] Add date of status change to session table #8350
• [candidate_parameters] Allow clearing of consent status by @CamilleBeau in [candidate_parameters] Allow clearing of consent status #7772
• [instruments/instrument_manager] Migrate instrument permissions from config.xml to database by @driusan in [instruments/instrument_manager] Migrate instrument permissions from config.xml to database #8302
• [Form.js] Add support for step to NumericElement by @driusan in [Form.js] Add support for step to NumericElement #8413
• [Form.js] Add placeholder option for TextareaElement by @driusan in [Form.js] Add placeholder option for TextareaElement #8412
• [Form.js] Add DateTimeElement wrapper by @driusan in [Form.js] Add DateTimeElement wrapper #8410
• [Form.js] Add support for vertical Radio button groups by @driusan in [Form.js] Add support for vertical Radio button groups #8414
• [DQT] add delete feature by @kongtiaowang in [DQT] add delete feature #8078
• [jsx/Panel.js] Improved Panel component with optional multiple views by @maltheism in [jsx/Panel.js] Improved Panel component with optional multiple views #8299
• [Issue tracker] change userID to full name by @regisoc in [Issue tracker] change userID to full name #8451
• [dashboard/statistics] Reactification by @laemtl in [dashboard/statistics] Reactification #8476
• [issue_tracker] Display attachments by @CamilleBeau in [issue_tracker] Display attachments #8346
• [API] Sites endpoint by @xlecours in [API] Sites endpoint #7771
• [EEG] EEG Acquisition form by @regisoc in [EEG] EEG Acquisition form #8443
• [Document Repository] Upload multiple files at once by @jeffersoncasimir in [Document Repository] Upload multiple files at once #8289
• [EEG] EEG uploader module by @laemtl in [EEG] EEG uploader module #8409
• [conflict_resolver/candidate_profile] Fix loading of conflict widget by @driusan in [conflict_resolver/candidate_profile] Fix loading of conflict widget #8569
• [media] changed permision check to media_read to enable media downloads by @KLaFleur in changed permision check to media_read to enable media downloads #8671
• [EEG Browser] Addition of new changes to signal plot of electrophysiology_browser module from EEGNet by @jeffersoncasimir in [EEG Browser] Addition of new changes to signal plot of electrophysiology_browser module from EEGNet #8415
• [Imaging Browser] Fix caveat bug not showing when there are pipeline protocol violations by @cmadjar in [Imaging Browser] Fix caveat bug not showing when there are pipeline protocol violations #8661
• [MRI violations] Fix multiple rows for file protocol violations not resolvable by @cmadjar in [MRI violations] Fix multiple rows for file protocol violations not resolvable #8662
• [candidate] Allow dob format Y-m by @CamilleBeau in [candidate] Allow dob format Y-m #8648
• [EEG Uploader] Handle Checksum value by @laemtl in [EEG Uploader] Handle Checksum value #8729
• [module_manager] Visibility of 'My Preferences' in menu reflects state by @jeffersoncasimir in [module_manager] Visibility of 'My Preferences' in menu reflects state #8726
• [new_profile] Fix date requirements and formats with EDC by @charlottesce in [new_profile] Fix date requirements and formats with EDC #8767
• [new_profile] DateElement in 'Y-m' Fix by @skarya22 in [new_profile] DateElement in 'Y-m' Fix #8775
• [Timepoint List] Hide visits that are from user unaffiliated projects by @skarya22 in [Timepoint List] Hide visits that are from user unaffiliated projects #8723
• [data_release] Permission not added to unversioned files if version specified by @charlottesce in [data_release] Permission not added to unversioned files if version specified #8768
• [battery_manager] use visit controller to fetch visit list by @ridz1208 in [battery_manager] use visit controller to fetch visit list #8485
• [Core] PSCID uniqueness by @xlecours in [Core] PSCID uniqueness #8411

New Contributors

• @satvik-tha-god made their first contribution in [RaisinBread] Fixed Candidate DoB and Date_registered entries #8146
• @jeffersoncasimir made their first contribution in [Docs - LORIS installation] Updated installation instructions to reflect the requirement of PHP 8.0+ #8223
• @violetwei made their first contribution in [candidate_list] Fix Typo 'VisitCount' to 'Visit Count'  #8321
• @GeorgeMurad made their first contribution in Flag_Status field in flag table appears to be unused #8278
• @KLaFleur made their first contribution in changed permision check to media_read to enable media downloads #8671
• @charlottesce made their first contribution in [Media] Fix Input callback not set #8720
• @skarya22 made their first contribution in [battery_manager] React warning messages in console #8724

Full Changelog: v24.1.4...v25.0.0

Notes For Existing Projects

• API: Modified in v0.0.4-dev the candidate instrument data format returned by a GET request or provided as the body of a PUT/PATCH request. The values of all fields are now defined by the Data key instead of $InstrumentName (PR [api] Modify YAML schema so that Swagger Codegen PHP Client works #7857)

Notes For Developers

• Require jsodc comments to have correct @return and @param values in javascript (PR Jsdoc update #8266)
• Disable ESLint on build (prod instances) (PR [ESLint] Disable on prod instances #8229)

Upgrade Process

24.1.x to 25

1. Get the 25.0.0 source code

2. Source the SQL/Release_patches/24.1_To_25.0_upgrade.sql SQL file into your database.

3. Run the following scripts:

   1. php tools/configuration_check.php
      This script is used to validate the configuration of LORIS. It checks configuration settings and server paths to make sure that the application and underlying architecture are set up to allow LORIS to run properly.
   2. php tools/single_use/migrate_instrument_permissions.php
      This script migrates instrument permissions from the config.xml to the new database tables that now store them.
   3. php tools/single_use/update_violations_resolved_hashes.sql.php
      This script is intended for a one-time use only to update the hasing of the violations_resolved table. Not doing so will result in duplication of data in the violations_resolved tale when users update a resolution status for a violation.

4. Run make all from the LORIS root directory.

5. OPTIONAL: Run any cleanup patches in SQL/Archive/25.0/Cleanup/

6. OPTIONAL: Remove the <instrumentPermissions> tag from your config.xml which is no longer used after running the migration script.

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This discussion was created from the release LORIS Release v25.0.0.