[candidate] Create Sex table and remove Sex enum (#9025)

This changes the datatype of the candidate table columns "Sex" and ProbandSex" from enum to varchar(255), instead creating a constraint on the columns determined by a new "sex" table. The "sex" table contains optional values for candidate sex and candidate proband sex. Projects can add or remove Sex options by simply inserting into or dropping from this table.
aces · Feb 12, 2024 · e2d6f04 · e2d6f04
1 parent 52162d1
commit e2d6f04
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Showing 22 changed files with 105 additions and 57 deletions.
diff --git a/.phan/config.php b/.phan/config.php
@@ -38,7 +38,7 @@
         "php",
         "htdocs",
         "modules",
-        "src",
+	"src",
         "vendor",
         "test"
     ],

diff --git a/CHANGELOG.md b/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)

diff --git a/SQL/0000-00-00-schema.sql b/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` (

diff --git a/SQL/New_patches/2024-01-29-create-sex-table.sql b/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 (Sex) 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;
diff --git a/modules/candidate_list/jsx/candidateListIndex.js b/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,
         },
       },
       {

diff --git a/modules/candidate_list/php/candidate_list.class.inc b/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(),
         ];
     }
 

diff --git a/modules/candidate_parameters/ajax/getData.php b/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;

diff --git a/modules/candidate_parameters/jsx/ProbandInfo.js b/modules/candidate_parameters/jsx/ProbandInfo.js
@@ -1,6 +1,14 @@
 import React, {Component} from 'react';
 import PropTypes from 'prop-types';
 import Loader from 'Loader';
+import {
+  FormElement,
+  StaticElement,
+  SelectElement,
+  ButtonElement,
+  DateElement,
+  TextareaElement,
+} from 'jsx/Form';
 
 /**
  * Proband Info Component.
@@ -16,11 +24,7 @@ class ProbandInfo extends Component {
     super(props);
 
     this.state = {
-      sexOptions: {
-        Male: 'Male',
-        Female: 'Female',
-        Other: 'Other',
-      },
+      sexOptions: {},
       Data: [],
       formData: {},
       updateResult: null,
@@ -66,6 +70,7 @@ class ProbandInfo extends Component {
           formData: formData,
           Data: data,
           isLoaded: true,
+          sexOptions: data.sexOptions,
         });
       },
       error: (error) => {

diff --git a/modules/candidate_parameters/php/candidatequeryengine.class.inc b/modules/candidate_parameters/php/candidatequeryengine.class.inc
@@ -4,6 +4,7 @@ namespace LORIS\candidate_parameters;
 use LORIS\Data\Scope;
 use LORIS\Data\Cardinality;
 use LORIS\Data\Dictionary\DictionaryItem;
+use LORIS\Data\Types\Enumeration;
 
 /**
  * A CandidateQueryEngine providers a QueryEngine interface to query
@@ -54,6 +55,8 @@ class CandidateQueryEngine extends \LORIS\Data\Query\SQLQueryEngine
             "Demographics",
             "Candidate Demographics",
         );
+        $sexList      = \Utility::getSexList();
+        $t            = new Enumeration(...$sexList);
         $demographics = $demographics->withItems(
             [
                 new DictionaryItem(
@@ -74,7 +77,7 @@ class CandidateQueryEngine extends \LORIS\Data\Query\SQLQueryEngine
                     "Sex",
                     "Candidate's biological sex",
                     $candscope,
-                    new \LORIS\Data\Types\Enumeration('Male', 'Female', 'Other'),
+                    $t,
                     new Cardinality(Cardinality::SINGLE),
                 ),
                 new DictionaryItem(

diff --git a/modules/genomic_browser/jsx/tabs_content/cnv.js b/modules/genomic_browser/jsx/tabs_content/cnv.js
@@ -137,10 +137,7 @@ class CNV extends Component {
         filter: {
           name: 'Sex',
           type: 'select',
-          options: {
-            Male: 'Male',
-            Female: 'Female',
-          },
+          options: options.Sex,
         },
       },
       {

diff --git a/modules/genomic_browser/jsx/tabs_content/methylation.js b/modules/genomic_browser/jsx/tabs_content/methylation.js
@@ -138,10 +138,7 @@ class Methylation extends Component {
         filter: {
           name: 'Sex',
           type: 'select',
-          options: {
-            Male: 'Male',
-            Female: 'Female',
-          },
+          options: options.Sex,
         },
       },
       {

diff --git a/modules/genomic_browser/jsx/tabs_content/profiles.js b/modules/genomic_browser/jsx/tabs_content/profiles.js
@@ -168,10 +168,7 @@ class Profiles extends Component {
         filter: {
           name: 'Sex',
           type: 'select',
-          options: {
-            Male: 'Male',
-            Female: 'Female',
-          },
+          options: options.Sex,
         },
       },
       {

diff --git a/modules/genomic_browser/jsx/tabs_content/snp.js b/modules/genomic_browser/jsx/tabs_content/snp.js
@@ -138,10 +138,7 @@ class SNP extends Component {
         filter: {
           name: 'Sex',
           type: 'select',
-          options: {
-            Male: 'Male',
-            Female: 'Female',
-          },
+          options: options.Sex,
         },
       },
       {

diff --git a/modules/genomic_browser/php/views/cnv.class.inc b/modules/genomic_browser/php/views/cnv.class.inc
@@ -43,6 +43,7 @@ class CNV
             'Sites'    => $sites,
             'Cohorts'  => $cohorts,
             'Platform' => $platform_options,
+            'Sex'      => \Utility::getSexList(),
         ];
     }
 

diff --git a/modules/genomic_browser/php/views/methylation.class.inc b/modules/genomic_browser/php/views/methylation.class.inc
@@ -57,6 +57,7 @@ class Methylation
                 'genotyping_platform',
                 'Name'
             ),
+            'Sex'             => \Utility::getSexList(),
         ];
     }
 

diff --git a/modules/genomic_browser/php/views/profiles.class.inc b/modules/genomic_browser/php/views/profiles.class.inc
@@ -41,6 +41,7 @@ class Profiles
         $this->_formElement = [
             'Sites'   => $sites,
             'Cohorts' => $cohorts,
+            'Sex'     => \Utility::getSexList(),
         ];
     }
 

diff --git a/modules/genomic_browser/php/views/snp.class.inc b/modules/genomic_browser/php/views/snp.class.inc
@@ -43,6 +43,7 @@ class SNP
             'Sites'    => $sites,
             'Cohorts'  => $cohorts,
             'Platform' => $platform_options,
+            'Sex'      => \Utility::getSexList(),
         ];
     }
 

diff --git a/modules/new_profile/php/new_profile.class.inc b/modules/new_profile/php/new_profile.class.inc
@@ -46,14 +46,11 @@ class New_Profile extends \NDB_Form
         $ageMin    = $config->getSetting('ageMin');
         $dobFormat = $config->getSetting('dobFormat');
         $edc       = $config->getSetting('useEDC');
-        $sex       = [
-            'Male'   => 'Male',
-            'Female' => 'Female',
-            'Other'  => 'Other',
-        ];
-        $pscidSet  = "false";
-        $minYear   = (isset($startYear, $ageMax)) ? $startYear - $ageMax : null;
-        $maxYear   = (isset($endYear, $ageMin)) ? $endYear - $ageMin : null;
+        $sex       = \Utility::getSexList();
+
+        $pscidSet = "false";
+        $minYear  = (isset($startYear, $ageMax)) ? $startYear - $ageMax : null;
+        $maxYear  = (isset($endYear, $ageMin)) ? $endYear - $ageMin : null;
 
         // Get sites for the select dropdown
         $user_list_of_sites = $user->getCenterIDs();

diff --git a/php/libraries/Utility.class.inc b/php/libraries/Utility.class.inc
@@ -125,6 +125,23 @@ class Utility
         return $result;
     }
 
+    /**
+     * Returns list of sex options in the database
+     *
+     * @return array An associative array of sex values.
+     */
+    static function getSexList(): array
+    {
+        $factory = NDB_Factory::singleton();
+        $DB      = $factory->database();
+
+        $query = "SELECT Name FROM sex";
+
+        $result = $DB->pselectCol($query, []);
+
+        return array_combine($result, $result);
+    }
+
     /**
      * Returns a list of sites in the database
      *

diff --git a/src/StudyEntities/Candidate/Sex.php b/src/StudyEntities/Candidate/Sex.php
@@ -28,11 +28,7 @@ class Sex implements \JsonSerializable
     /* @var string */
     public $value;
 
-    private const VALID_VALUES = array(
-                                  'Male',
-                                  'Female',
-                                  'Other',
-                                 );
+    private $validValues = [];
 
     /**
      * Calls validate() immediately.
@@ -43,10 +39,12 @@ class Sex implements \JsonSerializable
      */
     public function __construct(string $value)
     {
-        if (!self::validate($value)) {
+        $this->validValues = \Utility::getSexList();
+
+        if (!self::validate($value, $this->validValues)) {
             throw new \DomainException(
                 'The value is not valid. Must be one of: '
-                . implode(', ', self::VALID_VALUES)
+                . implode(', ', array_values($this->validValues))
             );
         }
         $this->value = $value;
@@ -55,13 +53,14 @@ public function __construct(string $value)
     /**
      * Ensures that the value is well-formed.
      *
-     * @param string $value The value to be validated
+     * @param string $value      The value to be validated
+     * @param array  $laidValues The restricted optional values of $value
      *
      * @return bool True if the value format is valid
      */
-    public static function validate(string $value): bool
+    public static function validate(string $value, array $validValues): bool
     {
-        return in_array($value, self::VALID_VALUES, true);
+        return in_array($value, array_values($validValues), true);
     }
 
     /**
-Original file line number
+Diff line change
@@ Expand Up / @@ -38,7 +38,7 @@ @@
             "php",
             "htdocs",
             "modules",
-            "src",
+    	"src",
             "vendor",
             "test"
         ],
@@ Expand Down @@