// FIXME; perhaps a HTTP/1.0 501 Not Implemented? If so, provide proper output (gene not found) and
// test if browsers show that output or their own error page. Also, then, use the same method at
// the bottom of all files, as a last resort if command/URL is not understood. Do all of this LATER.
exit;
}
}
define('PAGE_TITLE', 'View all screenings' . (isset($sGene) ? ' for gene ' . $sGene : ''));
$_T->printHeader();
$_T->printTitle();
$aColsToHide = array();
if (isset($sGene)) {
$aColsToHide[] = 'genes';
}
require ROOT_PATH . 'class/object_screenings.php';
$_DATA = new LOVD_Screening();
$_DATA->viewList('Screenings', $aColsToHide, false, false, (bool) ($_AUTH['level'] >= LEVEL_MANAGER), false, true);
$_T->printFooter();
exit;
}
if (PATH_COUNT == 2 && ctype_digit($_PE[1]) && !ACTION) {
// URL: /screenings/0000000001
// View specific entry.
$nID = sprintf('%010d', $_PE[1]);
define('PAGE_TITLE', 'View screening #' . $nID);
$_T->printHeader();
$_T->printTitle();
// Load appropriate user level for this screening entry.
lovd_isAuthorized('screening', $nID);
require ROOT_PATH . 'class/object_screenings.php';
$_DATA = new LOVD_Screening($nID);
$zData = $_DATA->viewEntry($nID);
$_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') {
// URL: /individuals?create
// Create a new entry.
$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, $_AUTH['id']))->fetchAssoc();
if (empty($zData)) {
define('PAGE_TITLE', 'Submit');
$_T->printHeader();
$_T->printTitle();
} 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') {
// URL: /users/00001?share_access
// Let the user share access to his objects to other users.
$nID = sprintf('%05d', $_PE[1]);
define('PAGE_TITLE', 'Sharing access');
define('LOG_EVENT', 'ShareAccess');
require_once ROOT_PATH . 'class/object_users.php';
require ROOT_PATH . 'inc-lib-form.php';
// Boolean flag setting whether users can give edit-permissions to their colleagues.
