Replace DoB/EDC with 'Derived Age'/'EDC Age'

SQL/0000-00-03-ConfigTables.sql

@@ -63,6 +63,7 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType,
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'dateDisplayFormat', 'The date format to use throughout LORIS for displaying date information - formats for date inputs are browser- and locale-dependent.', 1, 0, 'text', ID, 'Date display format', 28 FROM ConfigSettings WHERE Name="study";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'adminContactEmail', 'An email address that users can write to in order to report issues or ask question', 1, 0, 'text', ID, 'Administrator Email', 29 FROM ConfigSettings WHERE Name="study";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'UserMaximumDaysInactive', 'The maximum number of days since last login before making a user inactive', 1, 0, 'text', ID, 'Maximum Days Before Making User Inactive', 30 FROM ConfigSettings WHERE Name="study";
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'useDoB', 'Use DoB (Date of Birth)', 1, 0, 'boolean', ID, 'Use DoB', 31 FROM ConfigSettings WHERE Name="study";
 
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('paths', 'Specify directories where LORIS-related files are stored or created. Take care when editing these fields as changing them incorrectly can cause certain modules to lose functionality.', 1, 0, 'Paths', 2);
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'imagePath', 'Path to images for display in Imaging Browser (e.g. /data/$project/data/) ', 1, 0, 'text', ID, 'Images', 9 FROM ConfigSettings WHERE Name="paths";
@@ -188,6 +189,7 @@ INSERT INTO Config (ConfigID, Value) SELECT ID, "Example Study" FROM ConfigSetti
 INSERT INTO Config (ConfigID, Value) SELECT ID, "<h3>Example Study Description</h3>\r\n <p>This is a sample description for this study, because it is a new LORIS install that has not yet customized this text.</p>\r\n <p>A LORIS administrator can customize this text in the configuration module, under the configuration option labeled \"Study Description\"</p>\r\n <h3>Useful Links</h3>\r\n <ul>\r\n <li><a href=\"https://github.com/aces/Loris\" >LORIS GitHub Repository</a></li>\r\n <li><a href=\"https://github.com/aces/Loris/wiki/Setup\" >LORIS Setup Guide</a></li>\r\n <li><a href=\"https://www.youtube.com/watch?v=2Syd_BUbl5A\" >A video of a loris on YouTube</a></li>\r\n </ul>" FROM ConfigSettings WHERE Name="StudyDescription";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "images/neurorgb_web.jpg" FROM ConfigSettings WHERE Name="studylogo";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "false" FROM ConfigSettings WHERE Name="useEDC";
+INSERT INTO Config (ConfigID, Value) SELECT ID, "false" FROM ConfigSettings WHERE Name="useDoB";
 INSERT INTO Config (ConfigID, Value) SELECT ID, 8 FROM ConfigSettings WHERE Name="ageMin";
 INSERT INTO Config (ConfigID, Value) SELECT ID, 11 FROM ConfigSettings WHERE Name="ageMax";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "false" FROM ConfigSettings WHERE Name="useFamilyID";
@@ -288,4 +290,4 @@ INSERT INTO Config (ConfigID, Value) SELECT ID, ''  FROM ConfigSettings WHERE Na
 INSERT INTO Config (ConfigID, Value) SELECT ID, '' FROM ConfigSettings WHERE Name='bids_dataset_authors';
 INSERT INTO Config (ConfigID, Value) SELECT ID, '' FROM ConfigSettings WHERE Name='bids_acknowledgments_text';
 INSERT INTO Config (ConfigID, Value) SELECT ID, '' FROM ConfigSettings WHERE Name='bids_readme_text';
-INSERT INTO Config (ConfigID, Value) SELECT ID, '' FROM ConfigSettings WHERE Name='bids_validator_options_to_ignore';
+INSERT INTO Config (ConfigID, Value) SELECT ID, '' FROM ConfigSettings WHERE Name='bids_validator_options_to_ignore';

SQL/New_patches/2023-12-08_useDoB.sql

@@ -0,0 +1,2 @@
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'useDoB', 'Use DoB (Date of Birth)', 1, 0, 'boolean', ID, 'Use DoB', 31 FROM ConfigSettings WHERE Name="study";
+INSERT INTO Config (ConfigID, Value) SELECT ID, "false" FROM ConfigSettings WHERE Name="useDoB";

modules/candidate_profile/test/candidate_profileTest.php

@@ -11,6 +11,7 @@
  * @link     https://github.com/aces/Loris
  */
 use Facebook\WebDriver\WebDriverBy;
+
 require_once __DIR__
     . "/../../../test/integrationtests/LorisIntegrationTestWithCandidate.class.inc";
 /**
@@ -91,45 +92,23 @@ function testCandidateProfileWithoutProjectPermissions()
         $this->resetUserProject();
     }
     /**
-     * Test that the page instrument link works on card 2 section
+     * Test that the page instrument link works on card section
      *
      * @return void
      */
-    function testCandidateProfileInstrumentLink1()
+    function testCandidateProfileInstrumentLink()
     {
-        $this->safeGet($this->url . "/candidate_profile/900000/");
-        $this->safeFindElement(
+                $this->setupPermissions(['superuser']);
+
+        $this->safeGet($this->url . "/candidate_profile/115788/");
+        $this->safeClick(
             WebDriverBy::cssSelector(
-                "#card2 > div:nth-child(1) >".
-                "div:nth-child(1)>div:nth-child(1)>div:nth-child(1)>div:nth-".
-                "child(1)> div:nth-child(2) > h4:nth-child(1) > a:nth-child(1)"
+                '#card0 > div > div > div >'.
+                ' dl > div:nth-child(9) > dd > div > a:nth-child(1)'
             )
-        )->click();
-        $bodyText
-            = $this->safeFindElement(WebDriverBy::cssSelector("body"))
-            ->getText();
-        $this->assertStringContainsString(
-            "Behavioural Battery of Instruments",
-            $bodyText
         );
-    }
-    /**
-     * Test that the page instrument link works on card 1 section
-     *
-     * @return void
-     */
-    function testCandidateProfileInstrumentLink2()
-    {
-        $this->safeGet($this->url . "/candidate_profile/900000/");
-        $this->safeFindElement(
-            WebDriverBy::cssSelector(
-                "#card0 > div:nth-child(1) >".
-                "div:nth-child(1)>div:nth-child(1)>dl:nth-child(1)>div:nth-".
-                "child(9)>dd:nth-child(2) > div:nth-child(1) > a:nth-child(1)"
-            )
-        )->click();
-        $bodyText
-            = $this->safeFindElement(WebDriverBy::cssSelector("body"))
+
+        $bodyText = $this->safeFindElement(WebDriverBy::cssSelector("body"))
             ->getText();
         $this->assertStringContainsString(
             "Behavioural Battery of Instruments",

modules/configuration/php/cohort.class.inc

@@ -62,6 +62,11 @@ class Cohort extends \NDB_Form
                 '1' => 'Yes',
                 '0' => 'No',
             ];
+        $this->tpl_data['useDoBOptions']
+            = [
+                '1' => 'Yes',
+                '0' => 'No',
+            ];
 
         $this->tpl_data['WindowDifferenceOptions']
             = [

modules/instrument_list/php/instrument_list.class.inc

@@ -297,6 +297,26 @@ class Instrument_List extends \NDB_Menu_Filter
 
         $this->tpl_data['display']
             = array_merge($this->candidate->getData(), $this->timePoint->getData());
+        // DoB to Derived Age
+        $dob = $this->candidate->getCandidateDoB();
+        if (is_string($dob) && strtotime($dob) !== false) {
+            $dob_date     = new \DateTime($dob);
+            $current_date = new \DateTime();
+            $dob_year     = abs($current_date->diff($dob_date)->y);
+            $dob_month    = abs($current_date->diff($dob_date)->m);
+            $dob_age      = $dob_year . " y / " . $dob_month . " m";
+            $this->tpl_data['dob_age'] = $dob_age;
+        }
+        // EDC to EDC Age
+        $edc = $this->candidate->getCandidateEDC();
+        if (is_string($edc) && strtotime($edc) !== false) {
+            $edc_date     = new \DateTime($edc);
+            $current_date = new \DateTime();
+            $edc_year     = abs($current_date->diff($edc_date)->y);
+            $edc_month    = abs($current_date->diff($edc_date)->m);
+            $edc_age      = $edc_year . " y / " . $edc_month . " m";
+            $this->tpl_data['edc_age'] = $edc_age;
+        }
     }
 
     /**

modules/instrument_list/templates/menu_instrument_list.tpl

@@ -5,13 +5,11 @@
   <tr class="info">
     {assign var="DoB" value=$candidate->getDisplayDoB()}
     <th>
-      {$DoB['label']}
+      Derived Age
+    </th>
+    <th>
+        EDC Age
     </th>
-    {if $display.EDC!=""}
-      <th>
-        EDC
-      </th>
-    {/if}
     <th>
       Biological Sex
     </th>
@@ -69,13 +67,11 @@
   <tbody>
   <tr>
     <td>
-      {$DoB['value']}
+      {$dob_age}
+    </td>
+    <td>
+        {$edc_age}
     </td>
-    {if $display.EDC!=""}
-      <td>
-        {$display.EDC}
-      </td>
-    {/if}
     <td>
       {$display.Sex}
     </td>
@@ -247,4 +243,4 @@
     <button class="btn btn-primary" onclick="location.href='{$baseurl|default}/imaging_browser/viewSession/?sessionID={$sessionID}'">View Imaging data</button>
   </div>
 {/if}
-</div>
+</div>

modules/timepoint_list/php/timepoint_list.class.inc

@@ -80,8 +80,31 @@ class Timepoint_List extends \NDB_Menu
         $this->tpl_data['candID']    = $this->candID;
         $this->tpl_data['PSCID']     = $candidate->getPSCID();
         $this->tpl_data['candidate'] = $candidate->getData();
-        $this->tpl_data['cand']      = $candidate;
+        // convert DoB date to age and months and rename it to Derived Age
+        $dob = $candidate->getData();
+        if (isset($dob['DoB']) && is_string($dob['DoB'])) {
+            $dob_date = date_create_from_format('Y-m-d', $dob['DoB']);
+            if ($dob_date !== false) {
+                $current_date = new \DateTime();
+                $dob_year     = abs($current_date->diff($dob_date)->y);
+                $dob_month    = abs($current_date->diff($dob_date)->m);
+                $dob_age      = $dob_year . " y / " . $dob_month . " m";
+                $this->tpl_data['dob_age'] = $dob_age;
+            }
 
+        }
+        // convert EDC date to age and months and rename it to EDC Age
+        $edc = $candidate->getData();
+        if (isset($edc['EDC']) && is_string($edc['EDC'])) {
+            $edc_date = date_create_from_format('Y-m-d', $edc['EDC']);
+            if ($edc_date !== false) {
+                $current_date = new \DateTime();
+                $edc_year     = abs($current_date->diff($edc_date)->y);
+                $edc_month    = abs($current_date->diff($edc_date)->m);
+                $edc_age      = $edc_year . " y / " . $edc_month . " m";
+                $this->tpl_data['edc_age'] = $edc_age;
+            }
+        }
         $listOfSessionIDs = $candidate->getListOfTimePoints();
 
         $user     = \User::singleton();

modules/timepoint_list/templates/menu_timepoint_list.tpl

@@ -4,14 +4,11 @@
   <thead>
   <tr class="info">
     <th>
-    {assign var="DoB" value=$cand->getDisplayDoB()}
-    {$DoB['label']} 
+      Derived Age
+    </th>
+    <th>
+      EDC Age
     </th>
-    {if $candidate.EDC!=""}
-      <th>
-        EDC
-      </th>
-    {/if}
     <th>
       Biological Sex
     </th>
@@ -29,13 +26,11 @@
   <tbody>
   <tr>
     <td>
-      {$DoB['value']} 
+      {$dob_age}
+    </td>
+    <td>
+      {$edc_age}
     </td>
-    {if $candidate.EDC!=""}
-      <td>
-        {$candidate.EDC}
-      </td>
-    {/if}
     <td>
       {$candidate.Sex}
     </td>
@@ -159,4 +154,4 @@
         <tr><td colspan="10">You do not have access to any timepoints registered for this candidate.</td></tr>
     {/section}
     </tbody>
-</table>
+</table>

php/libraries/NDB_BVL_Instrument.class.inc

@@ -390,6 +390,27 @@ abstract class NDB_BVL_Instrument extends NDB_Page
 
         $this->tpl_data['candidate'] = $candidate->getData();
         $this->tpl_data['timePoint'] = $timePoint->getData();
+        // convert DoB And EDC date to years and months
+        // DoB to Derived Age
+        $dob = $candidate->getCandidateDoB();
+        if (is_string($dob) && strtotime($dob) !== false) {
+            $dob_date     = new \DateTime($dob);
+            $current_date = new \DateTime();
+            $dob_year     = abs($current_date->diff($dob_date)->y);
+            $dob_month    = abs($current_date->diff($dob_date)->m);
+            $dob_age      = $dob_year . " y / " . $dob_month . " m";
+            $this->tpl_data['dob_age'] = $dob_age;
+        }
+        // EDC to EDC Age
+        $edc = $candidate->getCandidateEDC();
+        if (is_string($edc) && strtotime($edc) !== false) {
+            $edc_date     = new DateTime($edc);
+            $current_date = new DateTime();
+            $edc_year     = abs($current_date->diff($edc_date)->y);
+            $edc_month    = abs($current_date->diff($edc_date)->m);
+            $edc_age      = $edc_year . " y / " . $edc_month . " m";
+            $this->tpl_data['edc_age'] = $edc_age;
+        }
     }
 
     /**

raisinbread/RB_files/RB_Config.sql

@@ -111,6 +111,7 @@ INSERT INTO `Config` (`ID`, `ConfigID`, `Value`) VALUES (124,128,'');
 INSERT INTO `Config` (`ID`, `ConfigID`, `Value`) VALUES (126,129,'365');
 INSERT INTO `Config` (`ID`, `ConfigID`, `Value`) VALUES (127,130,'/var/www/loris/');
 INSERT INTO `Config` (`ID`, `ConfigID`, `Value`) VALUES (128,131,'/data/EEGUploadIncomingPath/');
+INSERT INTO `Config` (`ID`, `ConfigID`, `Value`) VALUES (129,132,'false');
 
 UNLOCK TABLES;
 SET FOREIGN_KEY_CHECKS=1;

raisinbread/RB_files/RB_ConfigSettings.sql

@@ -120,8 +120,7 @@ INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMult
 INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`) VALUES (128,'default_cohort','Default cohort used when creating scan visit',1,0,'text',69,'Default cohort',13);
 INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`) VALUES (129,'UserMaximumDaysInactive','The maximum number of days since last login before making a user inactive.',1,0,'text',1,'Maximum Days Before Making User Inactive',30);
 INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`) VALUES (130,'DownloadPath','Where files are downloaded',1,0,'text',26,'Downloads',4);
-INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`) VALUES (131,'EEGUploadIncomingPath','Path to the upload directory for incoming EEG studies',1,0,'text',45,'EEG Incoming Directory',15);
-INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`) VALUES (132,'EEGS3DataPath','EEG S3 data path for assembly data',1,0,'text',45,'EEG S3 data path',15);
-
+INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`) VALUES (131,'EEGUploadIncomingPath', 'Path to the upload directory for incoming EEG studies', 1, 0, 'text', 26, 'EEG Incoming Directory', 15);
+INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`) VALUES (132,'useDoB','Use DoB (Date of Birth)',1,0,'boolean',1,'Use DoB',12);
 UNLOCK TABLES;
 SET FOREIGN_KEY_CHECKS=1;

raisinbread/test/api/LorisApiAuthenticatedTest.php

@@ -235,10 +235,9 @@ public function tearDown(): void
                 "CenterID" => '4',
             ],
         );
-
+        $this->DB->delete("flag", ['ID' => '999999']);
         $this->DB->delete("session", ['CandID' => '900000']);
         $this->DB->delete("candidate", ['CandID' => '900000']);
-        $this->DB->delete("flag", ['ID' => '999999']);
         $this->DB->delete("test_names", ['ID' => '999999']);
 
         $set = [

raisinbread/test/api/LorisApiAuthenticated_v0_0_3_Test.php

@@ -87,7 +87,25 @@ public function setUp(): void
                 'Active'                => 'Y',
                 'UserID'                => 1,
                 'Entity_type'           => 'Human',
-                'Sex'                   => 'Female'
+                'Sex'                   => 'Female',
+                'ExternalID'            => null,
+                'DoB'                   => '2003-10-31',
+                'DoD'                   => null,
+                'EDC'                   => '2003-11-30',
+                'Sex'                   => 'Male',
+                'Ethnicity'             => null,
+                'Active'                => 'Y',
+                'Date_active'           => '2016-01-23',
+                'RegisteredBy'          => null,
+                'Date_registered'       => '2016-01-23',
+                'flagged_caveatemptor'  => 'false',
+                'flagged_reason'        => null,
+                'flagged_other'         => null,
+                'flagged_other_status'  => null,
+                'Testdate'              => '2019-06-20 12:10:04',
+                'Entity_type'           => 'Human',
+                'ProbandSex'            => null,
+                'ProbandDoB'            => null
             ]
         );
         $this->DB->insert(

smarty/templates/instrument_html.tpl

@@ -14,13 +14,11 @@
   <thead>
   <tr class="info">
     <th>
-      DOB
+      Derived Age
+    </th>
+    <th>
+        EDC Age
     </th>
-    {if $candidate.EDC!=""}
-      <th>
-        EDC
-      </th>
-    {/if}
     <th>
       Biological Sex
     </th>
@@ -64,12 +62,14 @@
   <!-- candidate data -->
   <tbody>
   <tr>
-    <td>
-      {$candidate.DoB}
-    </td>
-    {if $candidate.EDC!=""}
+    {if $dob_age!=""}
+      <td>
+        {$dob_age}
+      </td>
+    {/if}
+    {if $edc_age!=""}
       <td>
-        {$candidate.EDC}
+        {$edc_age}
       </td>
     {/if}
     <td>