diff --git a/SQL/0000-00-00-schema.sql b/SQL/0000-00-00-schema.sql index 19fb5836987..63382061d7b 100644 --- a/SQL/0000-00-00-schema.sql +++ b/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, diff --git a/SQL/0000-00-03-ConfigTables.sql b/SQL/0000-00-03-ConfigTables.sql index 218649c0506..9a4d8f940d9 100644 --- a/SQL/0000-00-03-ConfigTables.sql +++ b/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"; diff --git a/SQL/New_patches/2025-12-16-remove-scan-done.sql b/SQL/New_patches/2025-12-16-remove-scan-done.sql new file mode 100644 index 00000000000..0f27f3b66a7 --- /dev/null +++ b/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'; diff --git a/modules/candidate_list/jsx/candidateListIndex.js b/modules/candidate_list/jsx/candidateListIndex.js index 36941ecae57..e85dfd293a3 100644 --- a/modules/candidate_list/jsx/candidateListIndex.js +++ b/modules/candidate_list/jsx/candidateListIndex.js @@ -152,12 +152,12 @@ class CandidateListIndex extends Component { default: return None; } } - if (column === this.props.t('Scan Done', {ns: 'loris'})) { + if (column === this.props.t('Scan Uploaded', {ns: 'loris'})) { if (cell === 'Y') { const pscid = row[this.props.t('PSCID', {ns: 'loris'})]; let url = this.props.baseURL + '/imaging_browser/?PSCID=' + pscid; return ( - + {this.props.t('Yes', {ns: 'loris'})} ); @@ -254,10 +254,10 @@ class CandidateListIndex extends Component { }, }, { - 'label': this.props.t('Scan Done', {ns: 'loris'}), + 'label': this.props.t('Scan Uploaded', {ns: 'loris'}), 'show': true, 'filter': { - name: 'scanDone', + name: 'scanUploaded', type: 'select', hide: this.state.hideFilter, options: { diff --git a/modules/candidate_list/php/candidatelistrowprovisioner.class.inc b/modules/candidate_list/php/candidatelistrowprovisioner.class.inc index 5c37df68c8e..69544c57dac 100644 --- a/modules/candidate_list/php/candidatelistrowprovisioner.class.inc +++ b/modules/candidate_list/php/candidatelistrowprovisioner.class.inc @@ -60,7 +60,10 @@ 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(f.FileID) > 0 THEN 'Y' + ELSE 'N' + END AS scanUploaded, 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 +84,7 @@ 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 WHERE c.Active = 'Y' AND c.RegistrationProjectID IS NOT NULL GROUP BY c.CandID, psc.Name, c.PSCID, c.Sex, c.Entity_type, diff --git a/modules/candidate_list/test/CandidateListTestIntegrationTest.php b/modules/candidate_list/test/CandidateListTestIntegrationTest.php index 0a22d67c065..176be1dc7d0 100644 --- a/modules/candidate_list/test/CandidateListTestIntegrationTest.php +++ b/modules/candidate_list/test/CandidateListTestIntegrationTest.php @@ -36,12 +36,12 @@ class CandidateListTestIntegrationTest extends LorisIntegrationTestWithCandidate static $cohort = 'select[name="cohort"]'; static $advancedFilter = ".panel-body .btn-primary:nth-child(1)"; // advanced filter - static $scanDone = 'select[name="scanDone"]'; - static $Participant = 'select[name="participantStatus"]'; - static $dob = 'input[name="DoB"]'; - static $visitCount = 'input[name="visitCount"]'; - static $feedback = 'select[name="feedback"]'; - static $edc = 'input[name="edc"]'; + static $scanUploaded = 'select[name="scanUploaded"]'; + static $Participant = 'select[name="participantStatus"]'; + static $dob = 'input[name="DoB"]'; + static $visitCount = 'input[name="visitCount"]'; + static $feedback = 'select[name="feedback"]'; + static $edc = 'input[name="edc"]'; @@ -136,10 +136,10 @@ function testCandidateListAdvancedOptionsAppear() $this->safeClick(WebDriverBy::cssSelector($btn)); // Go through each element and ensure it's on the page after clicking // advanced - $scanDoneOptions = $this->safeFindElement( - WebDriverBy::Name("scanDone") + $scanUploadedOptions = $this->safeFindElement( + WebDriverBy::Name("scanUploaded") ); - $this->assertEquals("select", $scanDoneOptions->getTagName()); + $this->assertEquals("select", $scanUploadedOptions->getTagName()); $participantsStatusOptions = $this->safeFindElement( WebDriverBy::Name("participantStatus") ); @@ -252,7 +252,7 @@ function testFilters() '210' ); $this->_filterTest( - self::$scanDone, + self::$scanUploaded, self::$display, self::$clearFilter, "Yes", @@ -357,23 +357,27 @@ function testPscidLink() } /** - * Tests that, click the scan_done ="y" link, + * Tests that, click the scanUploaded ="y" link, * and it will goto the imaging browser page. * * @return void */ - function testScanDoneLink() + function testScanUploadedLink() { $this->safeGet($this->url . "/candidate_list/?pscid=MTL022"); $bodyText = $this->safeFindElement( - WebDriverBy::cssSelector("#dynamictable > tbody > tr > td.scanDoneLink") + WebDriverBy::cssSelector( + "#dynamictable > tbody > tr > td.scanUploadedLink" + ) )->getText(); $this->assertStringContainsString( "Y", $bodyText ); $this->safeClick( - WebDriverBy::cssSelector("#dynamictable > tbody > tr > td.scanDoneLink") + WebDriverBy::cssSelector( + "#dynamictable > tbody > tr > td.scanUploadedLink" + ) ); $bodyText = $this->safeFindElement( WebDriverBy::cssSelector(self::$pscidLink) diff --git a/modules/electrophysiology_browser/test/EEGBrowserIntegrationTest.php b/modules/electrophysiology_browser/test/EEGBrowserIntegrationTest.php index 53025c17b84..21b97e198f0 100644 --- a/modules/electrophysiology_browser/test/EEGBrowserIntegrationTest.php +++ b/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', ] diff --git a/modules/imaging_browser/php/queryengine.class.inc b/modules/imaging_browser/php/queryengine.class.inc index 2b39b1cf2db..838dec9a471 100644 --- a/modules/imaging_browser/php/queryengine.class.inc +++ b/modules/imaging_browser/php/queryengine.class.inc @@ -196,8 +196,8 @@ class QueryEngine extends \LORIS\Data\Query\SQLQueryEngine ); $items = [ new DictionaryItem( - "ScanDone", - "Does the session have any imaging scan done?", + "ScanUploaded", + "Does the session have any imaging scan uploaded?", $scope, new \LORIS\Data\Types\BooleanType(), new Cardinality(Cardinality::SINGLE), @@ -374,11 +374,14 @@ class QueryEngine extends \LORIS\Data\Query\SQLQueryEngine protected function getFieldNameFromDict( \LORIS\Data\Dictionary\DictionaryItem $item ): string { - if ($item->getName() == 'ScanDone') { + if ($item->getName() == 'ScanUploaded') { $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"; + $this->addTable('LEFT JOIN files f ON (f.SessionID=s.ID)'); + return "EXISTS ( + SELECT 1 + FROM files f + WHERE f.SessionID = s.ID + )"; } if (!($item instanceof ImagingDictionaryItem)) { diff --git a/modules/imaging_browser/test/ImagingBrowserTestIntegrationTest.php b/modules/imaging_browser/test/ImagingBrowserTestIntegrationTest.php index 6c1dadc23b7..d117cdc759f 100644 --- a/modules/imaging_browser/test/ImagingBrowserTestIntegrationTest.php +++ b/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', ] diff --git a/modules/imaging_browser/test/ImagingQueryEngineTest.php b/modules/imaging_browser/test/ImagingQueryEngineTest.php index 8b7dd3f7f46..ee873d54533 100644 --- a/modules/imaging_browser/test/ImagingQueryEngineTest.php +++ b/modules/imaging_browser/test/ImagingQueryEngineTest.php @@ -107,8 +107,7 @@ function setUp() : void 'ProjectID' => 1, 'CohortID' => 1, 'Active' => 'Y', - 'Visit_Label' => 'TestMRIVisit', - 'Scan_Done' => 'Y' + 'Visit_Label' => 'TestMRIVisit' ], [ 'ID' => 2, @@ -117,8 +116,7 @@ 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 +127,7 @@ function setUp() : void 'ProjectID' => 1, 'CohortID' => 1, 'Active' => 'Y', - 'Visit_Label' => 'TestMRIVisit', - 'Scan_Done' => 'Y' + 'Visit_Label' => 'TestMRIVisit' ], ] ); @@ -225,13 +222,13 @@ function tearDown() : void } /** - * Test that matching ScanDone matches the correct CandIDs. + * Test that matching ScanUploaded matches the correct CandIDs. * * @return void */ - public function testScanDoneMatches() + public function testScanUploadedMatches() { - $dict = $this->_getDictItem("ScanDone"); + $dict = $this->_getDictItem("ScanUploaded"); $result = iterator_to_array( $this->engine->getCandidateMatches( @@ -239,15 +236,15 @@ public function testScanDoneMatches() ) ); - // 123456 has a ScanDone = true result for visit TestMRIVisit + // 123456 has a ScanUploaded = true result for visit TestMRIVisit // So does 123457. $this->assertTrue(is_array($result)); $this->assertEquals(2, count($result)); $this->assertEquals($result[0], new CandID("123456")); $this->assertEquals($result[1], new CandID("123457")); - // 123456 has a ScanDone = false result for visit TestBvlVisit - // No other candidate has a ScanDone=false session. + // 123456 has a ScanUploaded = false result for visit TestBvlVisit + // No other candidate has a ScanUploaded=false session. $result = iterator_to_array( $this->engine->getCandidateMatches( new QueryTerm($dict, new NotEqual(true)) @@ -385,7 +382,7 @@ function testGetCandidateData() $results = iterator_to_array( $this->engine->getCandidateData( [ - $this->_getDictItem("ScanDone"), + $this->_getDictItem("ScanUploaded"), $this->_getDictItem("ScanType1_file"), $this->_getDictItem("ScanType1_QCStatus"), ], @@ -394,13 +391,12 @@ function testGetCandidateData() ) ); - // 123458 had no files, but has a session, so still has the ScanDone - $this->assertEquals(count($results), 3); + $this->assertEquals(count($results), 1); $this->assertEquals( $results, [ "123456" => [ - "ScanDone" => [ + "ScanUploaded" => [ "1" => [ 'VisitLabel' => 'TestMRIVisit', 'SessionID' => 1, @@ -430,7 +426,7 @@ function testGetCandidateData() ], ], "123457" => [ - "ScanDone" => [ + "ScanUploaded" => [ "3" => [ 'VisitLabel' => 'TestMRIVisit', 'SessionID' => 3, @@ -461,7 +457,7 @@ function testGetCandidateData() ], ], "123458" => [ - 'ScanDone' => [], + 'ScanUploaded' => [], 'ScanType1_file' => [], 'ScanType1_QCStatus' => [], ], diff --git a/modules/instrument_list/php/instrument_list_controlpanel.class.inc b/modules/instrument_list/php/instrument_list_controlpanel.class.inc index 61070355ae7..9c72289784b 100644 --- a/modules/instrument_list/php/instrument_list_controlpanel.class.inc +++ b/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; } diff --git a/modules/instrument_list/templates/menu_instrument_list.tpl b/modules/instrument_list/templates/menu_instrument_list.tpl index 89199758ca4..8ba715f60fd 100644 --- a/modules/instrument_list/templates/menu_instrument_list.tpl +++ b/modules/instrument_list/templates/menu_instrument_list.tpl @@ -45,7 +45,7 @@ {dgettext("loris", "Cohort")} - {dgettext("timepoint_list", "Imaging Scan Done")} + {dgettext("timepoint_list", "Imaging Scan Uploaded")} {dgettext("instrument_list", "Within Optimal")} @@ -109,17 +109,17 @@ {$display.CohortTitle} - {if $display.Scan_done != ""} - {if $display.Scan_done == 'Y'} - {assign var="scan_done" value=dgettext("loris", "Yes")} + {if $display.scanUploaded != ""} + {if $display.scanUploaded == 'Y'} + {assign var="scanUploaded" value=dgettext("loris", "Yes")} - {$scan_done} + {$scanUploaded} {else} - {assign var="scan_done" value={dgettext("loris", "No")}} - {$scan_done} + {assign var="scanUploaded" value={dgettext("loris", "No")}} + {$scanUploaded} {/if} {else} - Data Missing + Data Missing {/if} diff --git a/modules/timepoint_list/php/timepoint_list.class.inc b/modules/timepoint_list/php/timepoint_list.class.inc index 844b3ee82fa..f5e04ea962e 100644 --- a/modules/timepoint_list/php/timepoint_list.class.inc +++ b/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]['scanUploaded'] + = $timePoint->isScanUploaded(); + $x++; } // end list diff --git a/modules/timepoint_list/templates/menu_timepoint_list.tpl b/modules/timepoint_list/templates/menu_timepoint_list.tpl index af55e861441..26d23024e2e 100644 --- a/modules/timepoint_list/templates/menu_timepoint_list.tpl +++ b/modules/timepoint_list/templates/menu_timepoint_list.tpl @@ -71,7 +71,7 @@ {dgettext("timepoint_list", "Stage Status")} {dgettext("timepoint_list", "Date of Stage")} {dgettext("loris", "Sent To DCC")} - {dgettext("timepoint_list", "Imaging Scan Done")} + {dgettext("timepoint_list", "Imaging Scan Uploaded")} {dgettext("loris", "Feedback")} {dgettext("timepoint_list", "BVL QC")} {dgettext("timepoint_list", "BVL Exclusion")} @@ -108,17 +108,17 @@ {/if} - {if $timePoints[timepoint].Scan_done != ""} - {if $timePoints[timepoint].Scan_done == 'Y'} - {assign var="scan_done" value={dgettext("loris", "Yes")}} + {if $timePoints[timepoint].scanUploaded != ""} + {if $timePoints[timepoint].scanUploaded} + {assign var="scanUploaded" value={dgettext("loris", "Yes")}} - {dgettext('loris', $scan_done)} + {dgettext('loris', $scanUploaded)} {else} - {assign var="scan_done" value={dgettext("loris", "No")}} - {$scan_done} + {assign var="scanUploaded" value={dgettext("loris", "No")}} + {$scanUploaded} {/if} {else} - Data Missing + Data Missing {/if} diff --git a/php/libraries/TimePoint.class.inc b/php/libraries/TimePoint.class.inc index a9d01c31c55..70c4eb15f4e 100644 --- a/php/libraries/TimePoint.class.inc +++ b/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['scanUploaded'] + = $this->isScanUploaded() ? '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 uploaded for this session * - * @return string 'Y' if a scan was done 'N' if not. + * @return bool */ - function getScanDone(): string + public function isScanUploaded() : bool { - return $this->_timePointInfo["Scan_done"]; + $db = \NDB_Factory::singleton()->database(); + $result = $db->pselectOne( + ' + SELECT COUNT(f.FileID) + FROM + files f + JOIN + session s ON s.ID=f.SessionID + WHERE + f.SessionID = :v_sessionid + ', + ['v_sessionid' => $this->getSessionID()] + ); + return $result > 0; } /** diff --git a/raisinbread/RB_files/RB_ConfigSettings.sql b/raisinbread/RB_files/RB_ConfigSettings.sql index 6bab02e3939..d98685f1a5e 100644 --- a/raisinbread/RB_files/RB_ConfigSettings.sql +++ b/raisinbread/RB_files/RB_ConfigSettings.sql @@ -19,7 +19,6 @@ INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMult INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (17,'excluded_instruments','Instruments to be excluded from the Data Dictionary and download via the Data Query Tool',1,1,'instrument',1,'Excluded instruments',16,0); INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (19,'InstrumentResetting','Allows resetting of instrument data',1,0,'boolean',1,'Instrument Resetting',18,0); INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (20,'SupplementalSessionStatus','Display supplemental session status information on Timepoint List page',1,0,'boolean',1,'Use Supplemental Session Status',19,0); -INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (21,'useScanDone','Used for identifying timepoints that have (or should have) imaging data',1,0,'boolean',1,'Use Scan Done',20,0); INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (22,'allowPrenatalTimepoints','Determines whether creation of timepoints prior to Date of Birth is allowed',1,0,'boolean',1,'Allow Prenatal Timepoints',21,0); INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (23,'ImagingUploaderAutoLaunch','Allows running the ImagingUpload pre-processing scripts',1,0,'boolean',1,'ImagingUploader Auto Launch',22,0); INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`, `Multilingual`) VALUES (24,'citation_policy','Citation Policy for Acknowledgements module',1,0,'textarea',1,'Citation Policy',23,0); diff --git a/raisinbread/RB_files/RB_session.sql b/raisinbread/RB_files/RB_session.sql index be7d6a824e5..7c7737593bc 100644 --- a/raisinbread/RB_files/RB_session.sql +++ b/raisinbread/RB_files/RB_session.sql @@ -1,1141 +1,1141 @@ SET FOREIGN_KEY_CHECKS=0; TRUNCATE TABLE `session`; LOCK TABLES `session` WRITE; -INSERT INTO `session` (`ID`, `CandidateID`, `CenterID`, `ProjectID`, `VisitNo`, `Visit_label`, `CohortID`, `Submitted`, `Current_stage`, `Date_stage_change`, `Screening`, `Date_screening`, `Visit`, `Date_visit`, `Date_status_change`, `Approval`, `Date_approval`, `Active`, `Date_active`, `RegisteredBy`, `UserID`, `Date_registered`, `Testdate`, `Hardcopy_request`, `BVLQCStatus`, `BVLQCType`, `BVLQCExclusion`, `QCd`, `Scan_done`, `MRIQCStatus`, `MRIQCPending`, `MRIQCFirstChangeTime`, `MRIQCLastChangeTime`, `MRICaveat`, `languageID`) VALUES (1,162,2,1,1,'V1',2,'N','Visit','2018-03-26',NULL,NULL,'In Progress','2018-03-26',NULL,NULL,NULL,'Y','2018-03-26','admin','admin','2018-03-26','2019-07-04 09:43:19','-',NULL,NULL,NULL,NULL,'N','','N',NULL,NULL,'false',NULL); 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+INSERT INTO `session` (`ID`, `CandidateID`, `CenterID`, `ProjectID`, `VisitNo`, `Visit_label`, `CohortID`, `Submitted`, `Current_stage`, `Date_stage_change`, `Screening`, `Date_screening`, `Visit`, `Date_visit`, `Date_status_change`, `Approval`, `Date_approval`, `Active`, `Date_active`, `RegisteredBy`, `UserID`, `Date_registered`, `Testdate`, `Hardcopy_request`, `BVLQCStatus`, `BVLQCType`, `BVLQCExclusion`, `QCd`, `MRIQCStatus`, `MRIQCPending`, `MRIQCFirstChangeTime`, `MRIQCLastChangeTime`, `MRICaveat`, `languageID`) VALUES (2146,1010,2,1,1,'V1',1,'N','Visit','2018-04-23',NULL,NULL,'In Progress','2018-04-15',NULL,NULL,NULL,'Y','2018-04-23','admin','admin','2018-04-23','2019-07-04 09:43:19','-',NULL,NULL,NULL,NULL,'','N',NULL,NULL,'false',NULL); +INSERT INTO `session` (`ID`, `CandidateID`, `CenterID`, `ProjectID`, `VisitNo`, `Visit_label`, `CohortID`, `Submitted`, `Current_stage`, `Date_stage_change`, `Screening`, `Date_screening`, `Visit`, `Date_visit`, `Date_status_change`, `Approval`, `Date_approval`, `Active`, `Date_active`, `RegisteredBy`, `UserID`, `Date_registered`, `Testdate`, `Hardcopy_request`, `BVLQCStatus`, `BVLQCType`, `BVLQCExclusion`, `QCd`, `MRIQCStatus`, `MRIQCPending`, `MRIQCFirstChangeTime`, `MRIQCLastChangeTime`, `MRICaveat`, `languageID`) VALUES (2147,1013,2,1,2,'V2',1,'N','Visit','2018-04-23',NULL,NULL,'In Progress','2018-04-19',NULL,NULL,NULL,'Y','2018-04-23','admin','admin','2018-04-23','2019-07-04 09:43:19','-',NULL,NULL,NULL,NULL,'','N',NULL,NULL,'false',NULL); +INSERT INTO `session` (`ID`, `CandidateID`, `CenterID`, `ProjectID`, `VisitNo`, `Visit_label`, `CohortID`, `Submitted`, `Current_stage`, `Date_stage_change`, `Screening`, `Date_screening`, `Visit`, `Date_visit`, `Date_status_change`, `Approval`, `Date_approval`, `Active`, `Date_active`, `RegisteredBy`, `UserID`, `Date_registered`, `Testdate`, `Hardcopy_request`, `BVLQCStatus`, `BVLQCType`, `BVLQCExclusion`, `QCd`, `MRIQCStatus`, `MRIQCPending`, `MRIQCFirstChangeTime`, `MRIQCLastChangeTime`, `MRICaveat`, `languageID`) VALUES (2148,1013,1,1,3,'V3',2,'N','Visit','2018-04-23',NULL,NULL,'In Progress','2018-03-03',NULL,NULL,NULL,'Y','2018-04-23','admin','admin','2018-04-23','2019-07-04 09:43:19','-',NULL,NULL,NULL,NULL,'','N',NULL,NULL,'false',NULL); +INSERT INTO `session` (`ID`, `CandidateID`, `CenterID`, `ProjectID`, `VisitNo`, `Visit_label`, `CohortID`, `Submitted`, `Current_stage`, `Date_stage_change`, `Screening`, `Date_screening`, `Visit`, `Date_visit`, `Date_status_change`, `Approval`, `Date_approval`, `Active`, `Date_active`, `RegisteredBy`, `UserID`, `Date_registered`, `Testdate`, `Hardcopy_request`, `BVLQCStatus`, `BVLQCType`, `BVLQCExclusion`, `QCd`, `MRIQCStatus`, `MRIQCPending`, `MRIQCFirstChangeTime`, `MRIQCLastChangeTime`, `MRICaveat`, `languageID`) VALUES (2149,1013,1,1,4,'V4',3,'N','Visit','2018-04-23',NULL,NULL,'In Progress','2018-04-04',NULL,NULL,NULL,'Y','2018-04-23','admin','admin','2018-04-23','2019-07-04 09:43:19','-',NULL,NULL,NULL,NULL,'','N',NULL,NULL,'false',NULL); +INSERT INTO `session` (`ID`, `CandidateID`, `CenterID`, `ProjectID`, `VisitNo`, `Visit_label`, `CohortID`, `Submitted`, `Current_stage`, `Date_stage_change`, `Screening`, `Date_screening`, `Visit`, `Date_visit`, `Date_status_change`, `Approval`, `Date_approval`, `Active`, `Date_active`, `RegisteredBy`, `UserID`, `Date_registered`, `Testdate`, `Hardcopy_request`, `BVLQCStatus`, `BVLQCType`, `BVLQCExclusion`, `QCd`, `MRIQCStatus`, `MRIQCPending`, `MRIQCFirstChangeTime`, `MRIQCLastChangeTime`, `MRICaveat`, `languageID`) VALUES (2150,1013,1,1,5,'V5',3,'N','Visit','2018-04-23',NULL,NULL,'In Progress','2018-04-05',NULL,NULL,NULL,'Y','2018-04-23','admin','admin','2018-04-23','2019-07-04 09:43:19','-',NULL,NULL,NULL,NULL,'','N',NULL,NULL,'false',NULL); +INSERT INTO `session` (`ID`, `CandidateID`, `CenterID`, `ProjectID`, `VisitNo`, `Visit_label`, `CohortID`, `Submitted`, `Current_stage`, `Date_stage_change`, `Screening`, `Date_screening`, `Visit`, `Date_visit`, `Date_status_change`, `Approval`, `Date_approval`, `Active`, `Date_active`, `RegisteredBy`, `UserID`, `Date_registered`, `Testdate`, `Hardcopy_request`, `BVLQCStatus`, `BVLQCType`, `BVLQCExclusion`, `QCd`, `MRIQCStatus`, `MRIQCPending`, `MRIQCFirstChangeTime`, `MRIQCLastChangeTime`, `MRICaveat`, `languageID`) VALUES (2151,1013,1,1,6,'V6',3,'N','Visit','2018-04-23',NULL,NULL,'In Progress','2018-04-06',NULL,NULL,NULL,'Y','2018-04-23','admin','admin','2018-04-23','2019-07-04 09:43:19','-',NULL,NULL,NULL,NULL,'','N',NULL,NULL,'false',NULL); +INSERT INTO `session` (`ID`, `CandidateID`, `CenterID`, `ProjectID`, `VisitNo`, `Visit_label`, `CohortID`, `Submitted`, `Current_stage`, `Date_stage_change`, `Screening`, `Date_screening`, `Visit`, `Date_visit`, `Date_status_change`, `Approval`, `Date_approval`, `Active`, `Date_active`, `RegisteredBy`, `UserID`, `Date_registered`, `Testdate`, `Hardcopy_request`, `BVLQCStatus`, `BVLQCType`, `BVLQCExclusion`, `QCd`, `MRIQCStatus`, `MRIQCPending`, `MRIQCFirstChangeTime`, `MRIQCLastChangeTime`, `MRICaveat`, `languageID`) VALUES (2152,1012,1,1,4,'V4',4,'N','Visit','2018-04-23',NULL,NULL,'In Progress','2018-01-04',NULL,NULL,NULL,'Y','2018-04-23','admin','admin','2018-04-23','2019-07-04 09:43:19','-',NULL,NULL,NULL,NULL,'','N',NULL,NULL,'false',NULL); +INSERT INTO `session` (`ID`, `CandidateID`, `CenterID`, `ProjectID`, `VisitNo`, `Visit_label`, `CohortID`, `Submitted`, `Current_stage`, `Date_stage_change`, `Screening`, `Date_screening`, `Visit`, `Date_visit`, `Date_status_change`, `Approval`, `Date_approval`, `Active`, `Date_active`, `RegisteredBy`, `UserID`, `Date_registered`, `Testdate`, `Hardcopy_request`, `BVLQCStatus`, `BVLQCType`, `BVLQCExclusion`, `QCd`, `MRIQCStatus`, `MRIQCPending`, `MRIQCFirstChangeTime`, `MRIQCLastChangeTime`, `MRICaveat`, `languageID`) VALUES (2153,1012,1,1,5,'V5',4,'N','Visit','2018-04-23',NULL,NULL,'In Progress','2018-01-05',NULL,NULL,NULL,'Y','2018-04-23','admin','admin','2018-04-23','2019-07-04 09:43:19','-',NULL,NULL,NULL,NULL,'','N',NULL,NULL,'false',NULL); +INSERT INTO `session` (`ID`, `CandidateID`, `CenterID`, `ProjectID`, `VisitNo`, `Visit_label`, `CohortID`, `Submitted`, `Current_stage`, `Date_stage_change`, `Screening`, `Date_screening`, `Visit`, `Date_visit`, `Date_status_change`, `Approval`, `Date_approval`, `Active`, `Date_active`, `RegisteredBy`, `UserID`, `Date_registered`, `Testdate`, `Hardcopy_request`, `BVLQCStatus`, `BVLQCType`, `BVLQCExclusion`, `QCd`, `MRIQCStatus`, `MRIQCPending`, `MRIQCFirstChangeTime`, `MRIQCLastChangeTime`, `MRICaveat`, `languageID`) VALUES (2154,1012,1,1,6,'V6',4,'N','Visit','2018-04-23',NULL,NULL,'In Progress','2018-01-06',NULL,NULL,NULL,'Y','2018-04-23','admin','admin','2018-04-23','2019-07-04 09:43:19','-',NULL,'Visual',NULL,NULL,'','N',NULL,NULL,'false',NULL); +INSERT INTO `session` (`ID`, `CandidateID`, `CenterID`, `ProjectID`, `VisitNo`, `Visit_label`, `CohortID`, `Submitted`, `Current_stage`, `Date_stage_change`, `Screening`, `Date_screening`, `Visit`, `Date_visit`, `Date_status_change`, `Approval`, `Date_approval`, `Active`, `Date_active`, `RegisteredBy`, `UserID`, `Date_registered`, `Testdate`, `Hardcopy_request`, `BVLQCStatus`, `BVLQCType`, `BVLQCExclusion`, `QCd`, `MRIQCStatus`, `MRIQCPending`, `MRIQCFirstChangeTime`, `MRIQCLastChangeTime`, `MRICaveat`, `languageID`) VALUES (2155,1014,1,1,1,'V1',1,'N','Visit','2018-04-25',NULL,NULL,'In Progress','2018-04-18',NULL,NULL,NULL,'Y','2018-04-25','admin','admin','2018-04-25','2019-07-04 09:43:19','-',NULL,NULL,NULL,NULL,'','N',NULL,NULL,'false',NULL); +INSERT INTO `session` (`ID`, `CandidateID`, `CenterID`, `ProjectID`, `VisitNo`, `Visit_label`, `CohortID`, `Submitted`, `Current_stage`, `Date_stage_change`, `Screening`, `Date_screening`, `Visit`, `Date_visit`, `Date_status_change`, `Approval`, `Date_approval`, `Active`, `Date_active`, `RegisteredBy`, `UserID`, `Date_registered`, `Testdate`, `Hardcopy_request`, `BVLQCStatus`, `BVLQCType`, `BVLQCExclusion`, `QCd`, `MRIQCStatus`, `MRIQCPending`, `MRIQCFirstChangeTime`, `MRIQCLastChangeTime`, `MRICaveat`, `languageID`) VALUES (2156,1014,1,1,2,'V2',1,'N','Visit','2018-04-25',NULL,NULL,'In Progress','2018-04-18',NULL,NULL,NULL,'Y','2018-04-25','admin','admin','2018-04-25','2019-07-04 09:43:19','-',NULL,NULL,NULL,NULL,'','N',NULL,NULL,'false',NULL); +INSERT INTO `session` (`ID`, `CandidateID`, `CenterID`, `ProjectID`, `VisitNo`, `Visit_label`, `CohortID`, `Submitted`, `Current_stage`, `Date_stage_change`, `Screening`, `Date_screening`, `Visit`, `Date_visit`, `Date_status_change`, `Approval`, `Date_approval`, `Active`, `Date_active`, `RegisteredBy`, `UserID`, `Date_registered`, `Testdate`, `Hardcopy_request`, `BVLQCStatus`, `BVLQCType`, `BVLQCExclusion`, `QCd`, `MRIQCStatus`, `MRIQCPending`, `MRIQCFirstChangeTime`, `MRIQCLastChangeTime`, `MRICaveat`, `languageID`) VALUES (2157,1014,1,1,3,'V3',1,'N','Visit','2018-04-25',NULL,NULL,'In Progress','2018-04-18',NULL,NULL,NULL,'Y','2018-04-25','admin','admin','2018-04-25','2019-07-04 09:43:19','-',NULL,NULL,NULL,NULL,'','N',NULL,NULL,'false',NULL); +INSERT INTO `session` (`ID`, `CandidateID`, `CenterID`, `ProjectID`, `VisitNo`, `Visit_label`, `CohortID`, `Submitted`, `Current_stage`, `Date_stage_change`, `Screening`, `Date_screening`, `Visit`, `Date_visit`, `Date_status_change`, `Approval`, `Date_approval`, `Active`, `Date_active`, `RegisteredBy`, `UserID`, `Date_registered`, `Testdate`, `Hardcopy_request`, `BVLQCStatus`, `BVLQCType`, `BVLQCExclusion`, `QCd`, `MRIQCStatus`, `MRIQCPending`, `MRIQCFirstChangeTime`, `MRIQCLastChangeTime`, `MRICaveat`, `languageID`) VALUES (2158,1014,1,1,4,'V4',3,'N','Visit','2018-04-25',NULL,NULL,'In Progress','2018-04-18',NULL,NULL,NULL,'Y','2018-04-25','admin','admin','2018-04-25','2019-07-04 09:43:19','-',NULL,NULL,NULL,NULL,'','N',NULL,NULL,'false',NULL); +INSERT INTO `session` (`ID`, `CandidateID`, `CenterID`, `ProjectID`, `VisitNo`, `Visit_label`, `CohortID`, `Submitted`, `Current_stage`, `Date_stage_change`, `Screening`, `Date_screening`, `Visit`, `Date_visit`, `Date_status_change`, `Approval`, `Date_approval`, `Active`, `Date_active`, `RegisteredBy`, `UserID`, `Date_registered`, `Testdate`, `Hardcopy_request`, `BVLQCStatus`, `BVLQCType`, `BVLQCExclusion`, `QCd`, `MRIQCStatus`, `MRIQCPending`, `MRIQCFirstChangeTime`, `MRIQCLastChangeTime`, `MRICaveat`, `languageID`) VALUES (2159,1014,1,1,5,'V5',4,'N','Visit','2018-04-25',NULL,NULL,'In Progress','2018-04-18',NULL,NULL,NULL,'Y','2018-04-25','admin','admin','2018-04-25','2019-07-04 09:43:19','-',NULL,NULL,NULL,NULL,'','N',NULL,NULL,'false',NULL); +INSERT INTO `session` (`ID`, `CandidateID`, `CenterID`, `ProjectID`, `VisitNo`, `Visit_label`, `CohortID`, `Submitted`, `Current_stage`, `Date_stage_change`, `Screening`, `Date_screening`, `Visit`, `Date_visit`, `Date_status_change`, `Approval`, `Date_approval`, `Active`, `Date_active`, `RegisteredBy`, `UserID`, `Date_registered`, `Testdate`, `Hardcopy_request`, `BVLQCStatus`, `BVLQCType`, `BVLQCExclusion`, `QCd`, `MRIQCStatus`, `MRIQCPending`, `MRIQCFirstChangeTime`, `MRIQCLastChangeTime`, `MRICaveat`, `languageID`) VALUES (2160,1014,1,1,6,'V6',4,'N','Visit','2018-04-25',NULL,NULL,'In Progress','2018-04-18',NULL,NULL,NULL,'Y','2018-04-25','admin','admin','2018-04-25','2019-07-04 09:43:19','-',NULL,NULL,NULL,NULL,'','N',NULL,NULL,'false',NULL); UNLOCK TABLES; SET FOREIGN_KEY_CHECKS=1; diff --git a/smarty/templates/instrument_html.tpl b/smarty/templates/instrument_html.tpl index 93a38607ba4..72ce1e606e1 100644 --- a/smarty/templates/instrument_html.tpl +++ b/smarty/templates/instrument_html.tpl @@ -56,7 +56,7 @@ {dgettext("loris", "Cohort")} - {dgettext("timepoint_list", "Imaging Scan Done")} + {dgettext("timepoint_list", "Imaging Scan Uploaded")} {dgettext("instrument_list", "Within Optimal")} @@ -111,16 +111,16 @@ {$timePoint.CohortTitle} - {if $timePoint.Scan_done != ""} - {if $timePoint.Scan_done == 'Y'} - {assign var="scan_done" value=dgettext("loris", "Yes")} - {$scan_done} + {if $timePoint.scanUploaded != ""} + {if $timePoint.scanUploaded == 'Y'} + {assign var="scanUploaded" value=dgettext("loris", "Yes")} + {$scanUploaded} {else} - {assign var="scan_done" value={dgettext("loris", "No")}} - {$scan_done} + {assign var="scanUploaded" value={dgettext("loris", "No")}} + {$scanUploaded} {/if} {else} - Data Missing + Data Missing {/if} diff --git a/test/fixtures/tables/NDB_BVL_FeedbackTest.xml b/test/fixtures/tables/NDB_BVL_FeedbackTest.xml index 0ed891eb2ae..ad83618df82 100644 --- a/test/fixtures/tables/NDB_BVL_FeedbackTest.xml +++ b/test/fixtures/tables/NDB_BVL_FeedbackTest.xml @@ -131,7 +131,6 @@ - Y N @@ -164,7 +163,6 @@ - N N @@ -197,7 +195,6 @@ - Y N @@ -230,7 +227,6 @@ - N N @@ -263,7 +259,6 @@ - N N diff --git a/tools/exporters/dataExtractor.php b/tools/exporters/dataExtractor.php index c308c0e6985..de3ad7e559d 100755 --- a/tools/exporters/dataExtractor.php +++ b/tools/exporters/dataExtractor.php @@ -123,7 +123,6 @@ 'BVLQCType', 'BVLQCExclusion', 'QCd', - 'Scan_done', 'MRIQCStatus', 'MRIQCPending', 'MRICaveat' diff --git a/tools/generate_project_statistics_csv.php b/tools/generate_project_statistics_csv.php index 5e08fb8c3e0..1b23dd7913e 100755 --- a/tools/generate_project_statistics_csv.php +++ b/tools/generate_project_statistics_csv.php @@ -32,7 +32,10 @@ $project_statistics['Project'] = $projectname; // Number of Scanning - Visits $project_statistics['Number of Scanning - Visits'] = $DB->pselectOne( - "select count(*) from session where Scan_done='Y'", + "SELECT COUNT(DISTINCT s.ID) + FROM session s + JOIN files f + ON f.SessionID = s.ID;", [] ); // Number of Sites