Merge branch 'main' into 2024_01_30_hed_tag_support

.github/workflows/loristest.yml

@@ -52,7 +52,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        php: ['8.1', '8.2']
+        php: ['8.1', '8.2', '8.3']
     steps:
       - uses: actions/checkout@v2
 
@@ -104,7 +104,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        php: ['8.1', '8.2']
+        php: ['8.1', '8.2', '8.3']
         apiversion: ['v0.0.3', 'v0.0.4-dev']
     steps:
     - uses: actions/checkout@v2
@@ -167,9 +167,8 @@ jobs:
         mysql ${{ env.DB_DATABASE}} -uroot -proot < SQL/0000-00-03-ConfigTables.sql
         mysql ${{ env.DB_DATABASE}} -uroot -proot < SQL/0000-00-04-Help.sql
         mysql ${{ env.DB_DATABASE}} -uroot -proot < SQL/0000-00-05-ElectrophysiologyTables.sql
-        find raisinbread/instruments/instrument_sql -name *.sql -exec sh -c "echo Sourcing {}; mysql ${{ env.DB_DATABASE}} -uroot -proot < {}" \;
+        find raisinbread/instruments/instrument_sql -name *.sql -not -name 9999-99-99-drop_instrument_tables.sql -exec sh -c "echo Sourcing {}; mysql ${{ env.DB_DATABASE}} -uroot -proot < {}" \;
         find raisinbread/RB_files/ -name *.sql -exec sh -c "echo Sourcing {}; mysql ${{ env.DB_DATABASE}} -uroot -proot < {}" \;
-
     - name: Source instrument schemas
       run: |
         find raisinbread/instruments/instrument_sql -name 0000-*.sql -exec sh -c "echo Sourcing {}; mysql ${{ env.DB_DATABASE}} -uroot -proot < {}" \;
@@ -210,7 +209,7 @@ jobs:
         fail-fast: false
         matrix:
             testsuite: ['integration']
-            php: ['8.1','8.2']
+            php: ['8.1','8.2', '8.3']
             ci_node_index: [0,1,2,3]
 
             include:
@@ -221,10 +220,14 @@ jobs:
               php: '8.1'
             - testsuite: 'static'
               php: '8.2'
+            - testsuite: 'static'
+              php: '8.3'
             - testsuite: 'unit'
               php: '8.1'
             - testsuite: 'unit'
               php: '8.2'
+            - testsuite: 'unit'
+              php: '8.3'
 
     steps:
     - uses: actions/checkout@v2

.phan/config.php

@@ -38,7 +38,7 @@
         "php",
         "htdocs",
         "modules",
-        "src",
+	"src",
         "vendor",
         "test"
     ],

CHANGELOG.md

@@ -13,6 +13,9 @@ changes in the following format: PR #1234***
 #### Features
 - Add OpenID Connect authorization support to LORIS (PR #8255)
 
+#### Updates and Improvements
+- Create new `sex` table to hold candidate sex options, and change Sex and ProbandSex columns of `candidate` table to a varchar(255) datatype that is restricted by the `sex` table (PR #9025)
+
 #### Bug Fixes
 - Fix examiner site display (PR #8967)
 - bvl_feedback updates in real-time (PR #8966)

Dockerfile.test.db

@@ -1,4 +1,4 @@
-FROM mysql:5.7
+FROM mariadb:10.5
 
 ARG BASE_DIR
 

SQL/0000-00-00-schema.sql

@@ -72,6 +72,13 @@ CREATE TABLE `language` (
 INSERT INTO language (language_code, language_label) VALUES
     ('en-CA', 'English');
 
+CREATE TABLE `sex` (
+  `Name` varchar(255) NOT NULL,
+  PRIMARY KEY `Name` (`Name`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COMMENT='Stores sex options available for candidates in LORIS';
+
+INSERT INTO sex (Name) VALUES ('Male'), ('Female'), ('Other');
+
 CREATE TABLE `users` (
   `ID` int(10) unsigned NOT NULL auto_increment,
   `UserID` varchar(255) NOT NULL default '',
@@ -151,7 +158,7 @@ CREATE TABLE `candidate` (
   `DoB` date DEFAULT NULL,
   `DoD` date DEFAULT NULL,
   `EDC` date DEFAULT NULL,
-  `Sex` enum('Male','Female','Other') DEFAULT NULL,
+  `Sex` varchar(255) DEFAULT NULL,
   `RegistrationCenterID` integer unsigned NOT NULL DEFAULT '0',
   `RegistrationProjectID` int(10) unsigned NOT NULL,
   `Ethnicity` varchar(255) DEFAULT NULL,
@@ -166,7 +173,7 @@ CREATE TABLE `candidate` (
   `flagged_other_status` enum('not_answered') DEFAULT NULL,
   `Testdate` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
   `Entity_type` enum('Human','Scanner') NOT NULL DEFAULT 'Human',
-  `ProbandSex` enum('Male','Female','Other') DEFAULT NULL,
+  `ProbandSex` varchar(255) DEFAULT NULL,
   `ProbandDoB` date DEFAULT NULL,
   PRIMARY KEY (`CandID`),
   UNIQUE KEY `ID` (`ID`),
@@ -175,9 +182,13 @@ CREATE TABLE `candidate` (
   KEY `CandidateActive` (`Active`),
   KEY `FK_candidate_2_idx` (`flagged_reason`),
   KEY `PSCID` (`PSCID`),
+  KEY `FK_candidate_sex_1` (`Sex`),
+  KEY `FK_candidate_sex_2` (`ProbandSex`),
   CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`),
   CONSTRAINT `FK_candidate_2` FOREIGN KEY (`flagged_reason`) REFERENCES `caveat_options` (`ID`) ON DELETE RESTRICT ON UPDATE CASCADE,
-  CONSTRAINT `FK_candidate_RegistrationProjectID` FOREIGN KEY (`RegistrationProjectID`) REFERENCES `Project` (`ProjectID`) ON UPDATE CASCADE
+  CONSTRAINT `FK_candidate_RegistrationProjectID` FOREIGN KEY (`RegistrationProjectID`) REFERENCES `Project` (`ProjectID`) ON UPDATE CASCADE,
+  CONSTRAINT `FK_candidate_sex_1` FOREIGN KEY (`Sex`) REFERENCES `sex` (`Name`) ON DELETE RESTRICT ON UPDATE CASCADE,
+  CONSTRAINT `FK_candidate_sex_2` FOREIGN KEY (`ProbandSex`) REFERENCES `sex` (`Name`) ON DELETE RESTRICT ON UPDATE CASCADE
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 
 CREATE TABLE `session` (

SQL/New_patches/2024-01-29-Physiological-Events-Replace-Annotations.sql

@@ -7,3 +7,11 @@ DROP TABLE physiological_annotation_label;
 DROP TABLE physiological_annotation_file;
 DROP TABLE physiological_annotation_file_type;
 
+-- Event files are always associated to Projects, sometimes exclusively (dataset-scope events.json files)
+-- Add ProjectID and make PhysiologicalFileID DEFAULT NULL (ProjectID should ideally not be NULLable)
+ALTER TABLE `physiological_event_file`
+  CHANGE `PhysiologicalFileID` `PhysiologicalFileID` int(10) unsigned DEFAULT NULL,
+  ADD COLUMN `ProjectID` int(10) unsigned DEFAULT NULL AFTER `PhysiologicalFileID`,
+  ADD KEY `FK_physiological_event_file_project_id` (`ProjectID`),
+  ADD CONSTRAINT `FK_physiological_event_file_project_id`
+    FOREIGN KEY (`ProjectID`) REFERENCES `Project` (`ProjectID`);

SQL/New_patches/2024-01-29-create-sex-table.sql

@@ -0,0 +1,14 @@
+CREATE TABLE `sex` (
+  `Name` varchar(255) NOT NULL,
+  PRIMARY KEY `Name` (`Name`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COMMENT='Stores sex options available for candidates in LORIS';
+
+INSERT INTO sex (Name) VALUES ('Male'), ('Female'), ('Other');
+
+ALTER TABLE candidate
+  MODIFY COLUMN sex varchar(255) DEFAULT NULL,
+  MODIFY COLUMN ProbandSex varchar(255) DEFAULT NULL,
+  ADD KEY `FK_candidate_sex_1` (`Sex`),
+  ADD KEY `FK_candidate_sex_2` (`ProbandSex`),
+  ADD CONSTRAINT `FK_candidate_sex_1` FOREIGN KEY (`Sex`) REFERENCES `sex` (`Name`) ON DELETE RESTRICT ON UPDATE CASCADE,
+  ADD CONSTRAINT `FK_candidate_sex_2` FOREIGN KEY (`ProbandSex`) REFERENCES `sex` (`Name`) ON DELETE RESTRICT ON UPDATE CASCADE;

jsx/Filter.js

@@ -1,12 +1,13 @@
 import React, {useEffect} from 'react';
 import PropTypes from 'prop-types';
 import {
-    SelectElement,
+    CheckboxElement,
     DateElement,
-    TextboxElement,
-    FormElement,
     FieldsetElement,
-    CheckboxElement,
+    FormElement,
+    NumericElement,
+    SelectElement,
+    TextboxElement,
 } from 'jsx/Form';
 
 /**

modules/battery_manager/jsx/batteryManagerForm.js

@@ -1,5 +1,12 @@
 import React, {Component} from 'react';
 import PropTypes from 'prop-types';
+import {
+    ButtonElement,
+    FormElement,
+    StaticElement,
+    SelectElement,
+    NumericElement,
+} from 'jsx/Form';
 
 /**
  * Battery Manager Form

modules/battery_manager/jsx/batteryManagerIndex.js

@@ -6,6 +6,7 @@ import Loader from 'Loader';
 import FilterableDataTable from 'FilterableDataTable';
 import Modal from 'Modal';
 import swal from 'sweetalert2';
+import {CTA} from 'jsx/Form';
 
 import BatteryManagerForm from './batteryManagerForm';
 

modules/candidate_list/jsx/candidateListIndex.js

@@ -282,11 +282,7 @@ class CandidateListIndex extends Component {
           name: 'sex',
           type: 'select',
           hide: this.state.hideFilter,
-          options: {
-            'Male': 'Male',
-            'Female': 'Female',
-            'Other': 'Other',
-          },
+          options: options.Sex,
         },
       },
       {

modules/candidate_list/php/candidate_list.class.inc

@@ -119,6 +119,7 @@ class Candidate_List extends \DataFrameworkMenu
             'cohort'            => $cohort_options,
             'participantstatus' => $participant_status_options,
             'useedc'            => $config->getSetting("useEDC"),
+            'Sex'               => \Utility::getSexList(),
         ];
     }
 

modules/candidate_parameters/ajax/getData.php

@@ -220,6 +220,7 @@ function getProbandInfoFields()
         'ageDifference'    => $ageDifference,
         'extra_parameters' => $extra_parameters,
         'parameter_values' => $parameter_values,
+        'sexOptions'       => \Utility::getSexList(),
     ];
 
     return $result;