// Array which will make up the form table.
$aForm = array(array('POST', '', '', '', '0%', '0', '100%'), array('', '', 'print', 'Enter your password for authorization'), array('', '', 'password', 'password', 20), array('', '', 'print', '<INPUT type="submit" value="Save variant list" onclick="lovd_AJAX_viewListSubmit(\'Screenings_' . $nID . '_removeVariants\', function () { $(\'#removeVariants\').submit(); }); return false;"> <INPUT type="submit" value="Cancel" onclick="window.location.href=\'' . lovd_getInstallURL() . ($bSubmit ? 'submit/screening/' : 'screenings/') . $nID . '\'; return false;" style="border : 1px solid #FF4422;">'));
lovd_viewForm($aForm);
$_T->printFooter();
exit;
}
if (PATH_COUNT == 2 && ctype_digit($_PE[1]) && ACTION == 'delete') {
// URL: /screenings/0000000001?delete
// Drop specific entry.
$nID = sprintf('%010d', $_PE[1]);
define('PAGE_TITLE', 'Delete screening information entry ' . $nID);
define('LOG_EVENT', 'ScreeningDelete');
lovd_isAuthorized('screening', $nID);
lovd_requireAUTH(LEVEL_CURATOR);
require ROOT_PATH . 'class/object_screenings.php';
$_DATA = new LOVD_Screening();
$zData = $_DATA->loadEntry($nID);
require ROOT_PATH . 'inc-lib-form.php';
$a = $_DB->query('SELECT variantid, screeningid FROM ' . TABLE_SCR2VAR . ' GROUP BY variantid HAVING COUNT(screeningid) = 1 AND screeningid = ?', array($nID))->fetchAllColumn();
$aVariantsRemovable = array();
if (!empty($a)) {
$aVariantsRemovable = $_DB->query('SELECT variantid FROM ' . TABLE_SCR2VAR . ' WHERE screeningid = ? AND variantid IN (?' . str_repeat(', ?', count($a) - 1) . ')', array_merge(array($nID), $a))->fetchAllColumn();
}
$nVariantsRemovable = count($aVariantsRemovable);
if (!empty($_POST)) {
lovd_errorClean();
// Mandatory fields.
if (empty($_POST['password'])) {
lovd_errorAdd('password', 'Please fill in the \'Enter your password for authorization\' field.');
}
// User had to enter his/her password for authorization.
}
if (PATH_COUNT == 4 && $_PE[1] == 'individual' && ctype_digit($_PE[2]) && $_PE[3] == 'screenings' && !ACTION) {
// URL: /submit/individual/00000001/screenings
// Let submitter select screening to add variant to.
$nID = sprintf('%08d', $_PE[2]);
define('PAGE_TITLE', 'Select screening to add variant to');
$_T->printHeader();
$_T->printTitle();
$bExists = $_DB->query('SELECT COUNT(*) FROM ' . TABLE_INDIVIDUALS . ' WHERE id = ?', array($nID))->fetchColumn();
if (!$bExists || !isset($_AUTH['saved_work']['submissions']['individual'][$nID])) {
lovd_showInfoTable('No such ID!', 'stop');
$_T->printFooter();
exit;
}
require ROOT_PATH . 'class/object_screenings.php';
$_DATA = new LOVD_Screening();
$_GET['search_individualid'] = $nID;
$_GET['page_size'] = '10';
$_DATA->setRowLink('Screenings_submissions', 'variants?create&target=' . $_DATA->sRowID);
$_DATA->viewList('Screenings_submissions', array('individualid', 'owned_by_', 'created_date'), false, false);
$_T->printFooter();
exit;
}
if (PATH_COUNT == 3 && $_PE[1] == 'screening' && ctype_digit($_PE[2]) && !ACTION) {
// URL: /submit/screening/00000001
// Screening submission
global $_DB, $_AUTH;
define('LOG_EVENT', 'SubmitScreening');
lovd_requireAUTH(LEVEL_SUBMITTER);
$nID = sprintf('%010d', $_PE[2]);
$zData = $_DB->query('SELECT * FROM ' . TABLE_SCREENINGS . ' WHERE id = ? AND created_by = ?', array($nID, $_AUTH['id']))->fetchAssoc();
$_GET['page_size'] = '10';
if ($_AUTH['id'] == $nID) {
$_DATA->setRowLink('Individuals_submissions', 'submit/individual/' . $_DATA->sRowID);
} else {
$_DATA->setRowLink('Individuals_submissions', 'individuals/' . $_DATA->sRowID);
}
$_DATA->viewList('Individuals_submissions', array('individualid', 'diseaseids', 'owned_by_', 'status'), false, false, true, false, true);
unset($_GET['search_individualid']);
} else {
lovd_showInfoTable('No submissions of individuals found!', 'stop');
}
$_T->printTitle('Screenings', 'H4');
$aUnfinished = !empty($zData['saved_work']['submissions']['screening']) ? array_keys($zData['saved_work']['submissions']['screening']) : array();
if (!empty($aUnfinished)) {
require ROOT_PATH . 'class/object_screenings.php';
$_DATA = new LOVD_Screening();
$_GET['search_screeningid'] = implode('|', $aUnfinished);
$_GET['page_size'] = '10';
if ($_AUTH['id'] == $nID) {
$_DATA->setRowLink('Screenings_submissions', 'submit/screening/' . $_DATA->sRowID);
} else {
$_DATA->setRowLink('Individuals_submissions', 'screenings/' . $_DATA->sRowID);
}
$_DATA->viewList('Screenings_submissions', array('owned_by_', 'created_date', 'edited_date'), false, false, true, false, true);
} else {
lovd_showInfoTable('No submissions of variant screenings found!', 'stop');
}
$_T->printFooter();
exit;
}
if (PATH_COUNT == 2 && ctype_digit($_PE[1]) && ACTION == 'share_access') {
$_DATA = new LOVD_Phenotype($nDiseaseID);
print '<B>' . $sName . ' (<A href="diseases/' . $nDiseaseID . '">' . $sSymbol . '</A>)</B> <A href="phenotypes?create&target=' . $nID . '&diseaseid=' . $nDiseaseID . '"><IMG src="gfx/plus.png"></A> Add phenotype for this disease';
$_DATA->viewList('Phenotypes_for_I_VE_' . $nDiseaseID, array('phenotypeid', 'individualid', 'diseaseid'), true, true);
}
}
unset($_GET['search_individualid']);
unset($_GET['search_diseaseid']);
} else {
lovd_showInfoTable('No phenotypes found for this individual!', 'stop');
}
if (count($zData['screeningids'])) {
$_GET['search_individualid'] = $nID;
print '<BR><BR>' . "\n\n";
$_T->printTitle('Screenings', 'H4');
require ROOT_PATH . 'class/object_screenings.php';
$_DATA = new LOVD_Screening();
$_DATA->setSortDefault('id');
$_DATA->viewList('Screenings_for_I_VE', array('screeningid', 'individualid', 'created_date', 'edited_date'), true, true);
unset($_GET['search_individualid']);
$_GET['search_screeningid'] = implode('|', $zData['screeningids']);
print '<BR><BR>' . "\n\n";
$_T->printTitle('Variants', 'H4');
require ROOT_PATH . 'class/object_custom_viewlists.php';
// VOG needs to be first, so it groups by the VOG ID.
$_DATA = new LOVD_CustomViewList(array('VariantOnGenome', 'Scr2Var', 'VariantOnTranscript'));
$_DATA->viewList('CustomVL_VOT_for_I_VE', array(), false, false, (bool) ($_AUTH['level'] >= LEVEL_MANAGER));
}
$_T->printFooter();
exit;
}
if (PATH_COUNT == 1 && ACTION == 'create') {
});
prevHash = hash;
} else {
// The viewList could have been resubmitted now, so reset this value (not very efficient).
$( '#VOT_' + hash ).attr('class', 'data bold');
}
}
}
</SCRIPT>
<?php
if (!empty($zData['screeningids'])) {
$_GET['search_screeningid'] = $zData['screeningids'];
print '<BR><BR>' . "\n\n";
$_T->printTitle('Screenings', 'H4');
require ROOT_PATH . 'class/object_screenings.php';
$_DATA = new LOVD_Screening();
$_DATA->viewList('Screenings_for_VOG_VE', array('individualid', 'created_date', 'edited_date'), true, true);
}
$_T->printFooter();
exit;
}
if ((empty($_PE[1]) || $_PE[1] == 'upload') && ACTION == 'create') {
// URL: variants?create
// URL: variants/upload?create
// Detect whether a valid target screening is given. We do this here so we
// don't have to duplicate this code for variants?create and variants/upload?create.
// We don't want to show an error message about the screening if the user isn't allowed to come here.
// 2012-07-10; 3.0-beta-07; Submitters are no longer allowed to add variants without individual data.
if (!isset($_GET['target']) && !lovd_isAuthorized('gene', $_AUTH['curates'], false)) {
lovd_requireAUTH(LEVEL_CURATOR);
}
