Removal of scan_done field in session table

SQL/0000-00-00-schema.sql

@@ -221,7 +221,6 @@ CREATE TABLE `session` (
   `BVLQCType` enum('Visual','Hardcopy') DEFAULT NULL,
   `BVLQCExclusion` enum('Excluded','Not Excluded') DEFAULT NULL,
   `QCd` enum('Visual','Hardcopy') DEFAULT NULL,
-  `Scan_done` enum('N','Y') DEFAULT NULL,
   `MRIQCStatus` enum('','Pass','Fail') NOT NULL DEFAULT '',
   `MRIQCPending` enum('Y','N') NOT NULL DEFAULT 'N',
   `MRIQCFirstChangeTime` datetime DEFAULT NULL,

SQL/0000-00-03-ConfigTables.sql

@@ -69,7 +69,6 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType,
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'excluded_instruments', "Instruments to be excluded from the Data Dictionary and download via the Data Query Tool", 1, 1, 'instrument', ID, 'Excluded instruments', 18 FROM ConfigSettings WHERE Name="study";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'InstrumentResetting', 'Allows resetting of instrument data', 1, 0, 'boolean', ID, 'Instrument Resetting', 20 FROM ConfigSettings WHERE Name="study";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'SupplementalSessionStatus', 'Display supplemental session status information on Timepoint List page', 1, 0, 'boolean', ID, 'Use Supplemental Session Status', 21 FROM ConfigSettings WHERE Name="study";
-INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'useScanDone', 'Used for identifying timepoints that have (or should have) imaging data', 1, 0, 'boolean', ID, 'Use Scan Done', 22 FROM ConfigSettings WHERE Name="study";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'allowPrenatalTimepoints', 'Determines whether creation of timepoints prior to Date of Birth is allowed', 1, 0, 'boolean', ID, 'Allow Prenatal Timepoints', 23 FROM ConfigSettings WHERE Name="study";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'ImagingUploaderAutoLaunch', "Allows running the ImagingUpload pre-processing scripts", 1, 0, 'boolean', ID, 'ImagingUploader Auto Launch',24 FROM ConfigSettings WHERE Name="study";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'citation_policy', 'Citation Policy for Acknowledgements module', 1, 0, 'textarea', ID, 'Citation Policy', 25 FROM ConfigSettings WHERE Name="study";
@@ -226,7 +225,6 @@ INSERT INTO Config (ConfigID, Value) SELECT ID, "false" FROM ConfigSettings WHER
 INSERT INTO Config (ConfigID, Value) SELECT ID, "false" FROM ConfigSettings WHERE Name="useScreening";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "false" FROM ConfigSettings WHERE Name="useConsent";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "false" FROM ConfigSettings WHERE Name="SupplementalSessionStatus";
-INSERT INTO Config (ConfigID, Value) SELECT ID, "true" FROM ConfigSettings WHERE Name="useScanDone";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "true" FROM ConfigSettings WHERE Name="allowPrenatalTimepoints";
 INSERT INTO Config (ConfigID, Value) SELECT ID, 0 FROM ConfigSettings WHERE Name="ImagingUploaderAutoLaunch";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "Customize this text with your citation policy (via Configuration module)" FROM ConfigSettings WHERE Name="citation_policy";

SQL/New_patches/2025-12-16-remove-scan-done.sql

@@ -0,0 +1,5 @@
+ALTER TABLE session DROP COLUMN scan_done;
+
+DELETE FROM Config WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name="useScanDone");
+
+DELETE FROM ConfigSettings WHERE Name='useScanDone';

modules/candidate_list/php/candidatelistrowprovisioner.class.inc

@@ -60,7 +60,14 @@ class CandidateListRowProvisioner extends \LORIS\Data\Provisioners\DBRowProvisio
                 psc.Name AS RegistrationSite,
                 GROUP_CONCAT(DISTINCT sp.title) AS Cohort,
                 c.Entity_type AS EntityType,
-                MAX(s.Scan_done) AS scanDone,
+                CASE
+                    WHEN COUNT(s.ID) = 0 THEN NULL
+                    WHEN COUNT(f.FileID) > 0
+                        OR COUNT(mu.UploadID) > 0
+                        OR COUNT(t.TarchiveID) > 0 
+                    THEN 'Y'
+                    ELSE 'N'
+                END AS scanDone,
                 COALESCE(pso.Description,'Active') AS ParticipantStatus,
                 DATE_FORMAT(c.DoB,'%Y-%m-%d') AS DoB,
                 DATE_FORMAT(c.Date_registered,'%Y-%m-%d') AS Date_registered,
@@ -81,6 +88,9 @@ class CandidateListRowProvisioner extends \LORIS\Data\Provisioners\DBRowProvisio
                         ON (ps.participant_status=pso.ID)
                     LEFT JOIN Project p ON (c.RegistrationProjectID=p.ProjectID)
                     LEFT JOIN cohort sp ON (s.CohortID=sp.CohortID)
+                    LEFT JOIN files f ON f.SessionID=s.ID
+                    LEFT JOIN mri_upload mu ON mu.SessionID=s.ID
+                    LEFT JOIN tarchive t ON t.SessionID=s.ID
                 WHERE c.Active = 'Y'
                 AND c.RegistrationProjectID IS NOT NULL
                 GROUP BY c.CandID, psc.Name, c.PSCID, c.Sex, c.Entity_type,

modules/candidate_list/test/CandidateListTestIntegrationTest.php

@@ -357,7 +357,7 @@ function testPscidLink()
     }
 
     /**
-     * Tests that, click the scan_done ="y" link,
+     * Tests that, click the scanDone ="y" link,
      * and it will goto the imaging browser page.
      *
      * @return void
@@ -366,14 +366,18 @@ function testScanDoneLink()
     {
         $this->safeGet($this->url . "/candidate_list/?pscid=MTL022");
         $bodyText = $this->safeFindElement(
-            WebDriverBy::cssSelector("#dynamictable > tbody > tr > td.scanDoneLink")
+            WebDriverBy::cssSelector(
+                "#dynamictable > tbody > tr > td.scanDoneLink"
+            )
         )->getText();
         $this->assertStringContainsString(
             "Y",
             $bodyText
         );
         $this->safeClick(
-            WebDriverBy::cssSelector("#dynamictable > tbody > tr > td.scanDoneLink")
+            WebDriverBy::cssSelector(
+                "#dynamictable > tbody > tr > td.scanDoneLink"
+            )
         );
         $bodyText = $this->safeFindElement(
             WebDriverBy::cssSelector(self::$pscidLink)

modules/electrophysiology_browser/test/EEGBrowserIntegrationTest.php

@@ -84,7 +84,6 @@ function setUp(): void
                 'Visit_label'   => 'Test0',
                 'CenterID'      => 253,
                 'ProjectID'     => 2,
-                'Scan_done'     => 'Y',
                 'Current_stage' => 'Visit',
                 'Visit'         => 'In Progress',
             ]

modules/imaging_browser/php/queryengine.class.inc

@@ -376,9 +376,11 @@ class QueryEngine extends \LORIS\Data\Query\SQLQueryEngine
     ): string {
         if ($item->getName() == 'ScanDone') {
             $this->addTable('LEFT JOIN session s ON (s.CandidateID=c.ID)');
-                return "CASE WHEN s.Scan_Done='Y' THEN true
-                             WHEN s.Scan_Done='N' THEN false
-                             ELSE NULL END";
+            return "(
+                EXISTS (SELECT 1 FROM files      f2 WHERE f2.SessionID = s.ID)
+             OR EXISTS (SELECT 1 FROM mri_upload m2 WHERE m2.SessionID = s.ID)
+             OR EXISTS (SELECT 1 FROM tarchive   t2 WHERE t2.SessionID = s.ID)
+            )";
         }
 
         if (!($item instanceof ImagingDictionaryItem)) {

modules/imaging_browser/test/ImagingBrowserTestIntegrationTest.php

@@ -129,7 +129,6 @@ public function setUp(): void
                 'Visit_label'   => 'Test0',
                 'CenterID'      => 1,
                 'ProjectID'     => 1,
-                'Scan_done'     => 'Y',
                 'Current_stage' => 'Visit',
                 'Visit'         => 'In Progress',
             ]
@@ -143,7 +142,6 @@ public function setUp(): void
                 'Visit_label'   => 'Test1',
                 'CenterID'      => 253,
                 'ProjectID'     => 1,
-                'Scan_done'     => 'Y',
                 'Current_stage' => 'Visit',
                 'Visit'         => 'In Progress',
             ]
@@ -157,7 +155,6 @@ public function setUp(): void
                 'Visit_label'   => 'Test2',
                 'CenterID'      => 254,
                 'ProjectID'     => 1,
-                'Scan_done'     => 'Y',
                 'Current_stage' => 'Visit',
                 'Visit'         => 'In Progress',
             ]

modules/imaging_browser/test/ImagingQueryEngineTest.php

@@ -80,18 +80,6 @@ function setUp() : void
                     'EDC'                   => '1930-04-01',
                     'Entity_type'           => 'Human',
                 ],
-                [
-                    'ID'                    => 3,
-                    'CandID'                => "123458",
-                    'PSCID'                 => "test3",
-                    'RegistrationProjectID' => '1',
-                    'RegistrationCenterID'  => '3',
-                    'Active'                => 'N',
-                    'DoB'                   => '1940-01-01',
-                    'Sex'                   => 'Other',
-                    'EDC'                   => '1930-04-01',
-                    'Entity_type'           => 'Human',
-                ],
             ]
         );
 
@@ -107,8 +95,7 @@ function setUp() : void
                     'ProjectID'   => 1,
                     'CohortID'    => 1,
                     'Active'      => 'Y',
-                    'Visit_Label' => 'TestMRIVisit',
-                    'Scan_Done'   => 'Y'
+                    'Visit_Label' => 'TestMRIVisit'
                 ],
                 [
                     'ID'          => 2,
@@ -117,8 +104,7 @@ function setUp() : void
                     'ProjectID'   => 1,
                     'CohortID'    => 1,
                     'Active'      => 'Y',
-                    'Visit_Label' => 'TestBvlVisit',
-                    'Scan_Done'   => 'N'
+                    'Visit_Label' => 'TestBvlVisit'
                 ],
                 // Candidate 123457 has 1 visit with different MRI data
                 // It contains multiple ScanType1 and no ScanType2
@@ -129,8 +115,7 @@ function setUp() : void
                     'ProjectID'   => 1,
                     'CohortID'    => 1,
                     'Active'      => 'Y',
-                    'Visit_Label' => 'TestMRIVisit',
-                    'Scan_Done'   => 'Y'
+                    'Visit_Label' => 'TestMRIVisit'
                 ],
             ]
         );
@@ -389,13 +374,12 @@ function testGetCandidateData()
                     $this->_getDictItem("ScanType1_file"),
                     $this->_getDictItem("ScanType1_QCStatus"),
                 ],
-                [new CandID("123456"), new CandID("123457"), new CandID("123458")],
+                [new CandID("123456"), new CandID("123457")],
                 null
             )
         );
 
-        // 123458 had no files, but has a session, so still has the ScanDone
-        $this->assertEquals(count($results), 3);
+        $this->assertEquals(count($results), 2);
         $this->assertEquals(
             $results,
             [
@@ -460,11 +444,6 @@ function testGetCandidateData()
                         ],
                     ],
                 ],
-                "123458" => [
-                    'ScanDone'           => [],
-                    'ScanType1_file'     => [],
-                    'ScanType1_QCStatus' => [],
-                ],
             ]
         );
     }

modules/instrument_list/php/instrument_list_controlpanel.class.inc

@@ -635,11 +635,7 @@ class Instrument_List_ControlPanel extends \TimePoint
     function _getSendToDCCStatusMessage()
     {
         // create user object
-        $user   = \User::singleton();
-        $config = \NDB_Config::singleton();
-
-        // get the value of the session.Scan_done field
-        $scanDone = $this->getData('Scan_done');
+        $user = \User::singleton();
 
         if (!$user->hasPermission('send_to_dcc')) {
             return "User does not have permission to send to DCC";
@@ -674,12 +670,6 @@ class Instrument_List_ControlPanel extends \TimePoint
             return "The status of this stage is either"
                 . " In Progress or has not been set.";
         }
-        if (! $config->settingEnabled("useScanDone")
-            || ($this->getData('Current_stage') != 'Screening'
-            && empty($scanDone))
-        ) {
-            return "The Scan done field must be entered for the Visit stage";
-        }
 
         $battery = new \NDB_BVL_Battery();
 
@@ -734,11 +724,7 @@ class Instrument_List_ControlPanel extends \TimePoint
     function _hasAccessSendToDCC()
     {
         // create user object
-        $user   =& \User::singleton();
-        $config =& \NDB_Config::singleton();
-
-        // get the value of the session.Scan_done field
-        $scanDone = $this->getData('Scan_done');
+        $user =& \User::singleton();
 
         // make the option available is the Stage/Status is Sendable to DCC
         // or if its Superuser and option was Sent (to unsend i.e. set to N)
@@ -764,9 +750,6 @@ class Instrument_List_ControlPanel extends \TimePoint
                     'In Progress',
                 ]
             )
-            && (!$config->settingEnabled("useScanDone")
-            || $this->getData('Current_stage') == 'Screening'
-            || !empty($scanDone))
         ) {
             return true;
         }

modules/instrument_list/templates/menu_instrument_list.tpl

@@ -109,17 +109,17 @@
         {$display.CohortTitle}
       </td>
       <td>
-        {if $display.Scan_done != ""}
-            {if $display.Scan_done == 'Y'}
-                {assign var="scan_done" value=dgettext("loris", "Yes")}
+        {if $display.scanDone != ""}
+            {if $display.scanDone == 'Y'}
+                {assign var="scanDone" value=dgettext("loris", "Yes")}
                 <a href="{$baseurl|default}/imaging_browser/viewSession/?sessionID={$sessionID}" class="timepoint_list">
-                {$scan_done}</a>
+                {$scanDone}</a>
             {else}
-                {assign var="scan_done" value={dgettext("loris", "No")}}
-                {$scan_done}
+                {assign var="scanDone" value={dgettext("loris", "No")}}
+                {$scanDone}
             {/if}
         {else}
-            <img alt="Data Missing" src="{$baseurl|default}/images/help2.gif" border=0>
+            <img alt="Data Missing" src="{$baseurl|default}/images/delete.gif" border=0>
         {/if}
       </td>
       <td>

modules/timepoint_list/php/timepoint_list.class.inc

@@ -233,6 +233,10 @@ class Timepoint_List extends \NDB_Menu
 
             $this->tpl_data['timePoints'][$x]['language']
                 = $timePoint->getLanguage();
+
+            $this->tpl_data['timePoints'][$x]['scanDone']
+                =   $timePoint->isScanDone();
+
             $x++;
         } // end list
 

modules/timepoint_list/templates/menu_timepoint_list.tpl

@@ -108,17 +108,17 @@
             {/if}
             </td>
             <td>
-            {if $timePoints[timepoint].Scan_done != ""}
-                    {if $timePoints[timepoint].Scan_done == 'Y'}
-                        {assign var="scan_done" value={dgettext("loris", "Yes")}}
+            {if $timePoints[timepoint].scanDone != ""}
+                    {if $timePoints[timepoint].scanDone}
+                        {assign var="scanDone" value={dgettext("loris", "Yes")}}
                         <a href="{$baseurl|default}/imaging_browser/viewSession/?sessionID={$timePoints[timepoint].SessionID}" class="timepoint_list">
-                        {dgettext('loris', $scan_done)}</a>
+                        {dgettext('loris', $scanDone)}</a>
                     {else}
-                        {assign var="scan_done" value={dgettext("loris", "No")}}
-                        {$scan_done}
+                        {assign var="scanDone" value={dgettext("loris", "No")}}
+                        {$scanDone}
                     {/if}
             {else}
-                <img alt="Data Missing" src="{$baseurl|default}/images/help2.gif" border=0>
+                <img alt="Data Missing" src="{$baseurl|default}/images/delete.gif" border=0>
             {/if}
             </td>
 

php/libraries/TimePoint.class.inc

@@ -144,7 +144,7 @@ class TimePoint implements \LORIS\StudyEntities\AccessibleResource,
                          s.Current_stage, s.Screening, s.Date_screening, s.Visit,
                          s.Date_visit, s.Approval, s.Date_approval, s.Active,
                          s.registeredBy, s.UserID, u.Real_name, s.Hardcopy_request,
-                         s.BVLQCStatus, s.BVLQCType, s.BVLQCExclusion, s.Scan_done,
+                         s.BVLQCStatus, s.BVLQCType, s.BVLQCExclusion,
                          pr.Name as ProjectName, p.Alias as SiteAlias,
 			 s.ProjectID as ProjectID,
                          l.language_code as LanguageCode,
@@ -164,7 +164,7 @@ class TimePoint implements \LORIS\StudyEntities\AccessibleResource,
         $this->data = new TimePointData(
             $sessionID,
             isset($row['ProjectID'])
-                ? ProjectID::singleton($row['ProjectID'])
+                ? ProjectID::singleton((int) $row['ProjectID'])
                 : null,
             isset($row['CenterID'])
                 ? \CenterID::singleton($row['CenterID'])
@@ -189,6 +189,10 @@ class TimePoint implements \LORIS\StudyEntities\AccessibleResource,
 
             $this->_timePointInfo['CandID']
                 = new CandID(strval($row['CandID']));
+
+            $this->_timePointInfo['scanDone']
+                = $this->isScanDone() ? 'Y' : 'N';
+
         } else {
             // return error when 0 rows to prevent creation of an empty object
             throw new LorisException(
@@ -591,13 +595,26 @@ class TimePoint implements \LORIS\StudyEntities\AccessibleResource,
     }
 
     /**
-     * Gets whether or not a scan was done for this TimePoint
+     * Returns whether a scan has been done for this session
      *
-     * @return string 'Y' if a scan was done 'N' if not.
+     * @return bool
      */
-    function getScanDone(): string
+    public function isScanDone() : bool
     {
-        return $this->_timePointInfo["Scan_done"];
+        $db     = \NDB_Factory::singleton()->database();
+        $result = $db->pselectOne(
+            "SELECT DISTINCT 'Y' AS ScanDone
+            FROM session s
+            LEFT JOIN files       f  ON f.SessionID  = s.ID
+            LEFT JOIN mri_upload mu ON mu.SessionID = s.ID
+            LEFT JOIN tarchive    t  ON t.SessionID  = s.ID
+            WHERE s.ID = :v_sessionid
+              AND (f.FileID IS NOT NULL
+                   OR mu.UploadID IS NOT NULL
+                   OR t.TarchiveID IS NOT NULL)",
+            ['v_sessionid' => $this->getSessionID()]
+        );
+        return $result == 'Y';
     }
 
     /**