[candidate] Create Sex table and remove Sex enum

CamilleBeau · Jan 29, 2024 · 60309a5 · 60309a5
1 parent d0982ce
commit 60309a5
Show file tree

Hide file tree

Showing 18 changed files with 71 additions and 50 deletions.
diff --git a/SQL/0000-00-00-schema.sql b/SQL/0000-00-00-schema.sql
@@ -72,6 +72,15 @@ CREATE TABLE `language` (
 INSERT INTO language (language_code, language_label) VALUES
     ('en-CA', 'English');
 
+CREATE TABLE `sex` (
+  `SexID` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `SexValue` varchar(255) NOT NULL,
+  PRIMARY KEY (`SexID`),
+  UNIQUE KEY `SexValue` (`SexValue`)
+) ENGINE=InnoDB AUTO_INCREMENT=1 DEFAULT CHARSET=utf8 COMMENT='Stores sex options available for candidates in LORIS';
+
+INSERT INTO sex (SexValue) VALUES ('Male'), ('Female'), ('Other');
+
 CREATE TABLE `users` (
   `ID` int(10) unsigned NOT NULL auto_increment,
   `UserID` varchar(255) NOT NULL default '',
@@ -151,7 +160,7 @@ 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 +175,7 @@ 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 +184,13 @@ 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` (`SexValue`) ON DELETE RESTRICT ON UPDATE CASCADE,
+  CONSTRAINT `FK_candidate_sex_2` FOREIGN KEY (`ProbandSex`) REFERENCES `sex` (`SexValue`) ON DELETE RESTRICT ON UPDATE CASCADE
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 
 CREATE TABLE `session` (

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
@@ -74,7 +74,7 @@ class CandidateQueryEngine extends \LORIS\Data\Query\SQLQueryEngine
                     "Sex",
                     "Candidate's biological sex",
                     $candscope,
-                    new \LORIS\Data\Types\Enumeration('Male', 'Female', 'Other'),
+                    new \LORIS\Data\Types\StringType(255),
                     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 SexValue 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(', ', $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, $validValues, true);
     }
 
     /**

diff --git a/tools/CouchDB_Import_Demographics.php b/tools/CouchDB_Import_Demographics.php
@@ -48,7 +48,7 @@ class CouchDBDemographicsImporter
         ],
         'Sex'              => [
             'Description' => 'Candidate\'s biological sex',
-            'Type'        => "enum('Male', 'Female', 'Other')"
+            'Type'        => "varchar(255)"
         ],
         'Site'             => [
             'Description' => 'Site that this visit took place at',
@@ -324,7 +324,7 @@ function _updateDataDict()
         if ($config->getSetting("useProband") === "true") {
             $this->Dictionary["Sex_proband"]    = [
                 'Description' => 'Proband\'s biological sex',
-                'Type'        => "enum('Male','Female', 'Other')"
+                'Type'        => "varchar(255)"
             ];
             $this->Dictionary["Age_difference"] = [
                 'Description' => 'Age difference between the candidate and ' .
-Original file line number
+Diff line change
@@ Expand Up / @@ -57,6 +57,7 @@ class Methylation @@
                     'genotyping_platform',
                     'Name'
                 ),
+                'Sex'             => \Utility::getSexList(),
             ];
         }
@@ Expand Down @@