} if (!empty($aCategories['VariantOnGenome'])) { require ROOT_PATH . 'class/object_genome_variants.php'; $_DATAvariants = new LOVD_GenomeVariant(); } if (!empty($aCategories['Individual'])) { require ROOT_PATH . 'class/object_individuals.php'; $_DATAindividuals = new LOVD_Individual(); } print ' <SCRIPT type="text/javascript">' . "\n" . ' $(function() {' . "\n" . ' $("#tabs").tabs({active: ' . $nActiveTab . ', disabled: [' . $nDisabledTab . ']});' . "\n" . ' });' . "\n" . ' </SCRIPT>' . "\n" . ' <DIV id="tabs">' . "\n" . ' <UL>' . "\n" . ' <LI><A href="' . lovd_getInstallURL() . implode('/', $_PE) . '#tabs-variants">Variants</A></LI>' . "\n" . ' <LI><A href="' . lovd_getInstallURL() . implode('/', $_PE) . '#tabs-individuals">Individuals</A></LI>' . "\n" . ' </UL>' . "\n" . ' <DIV id="tabs-variants">' . "\n"; if (!empty($_DATAvariants)) { $_DATAvariants->viewList('Variants_per_reference', $aColsToHide['VariantOnGenome'], true, true); } print ' </DIV>' . "\n" . ' <DIV id="tabs-individuals">' . "\n"; if (!empty($_DATAindividuals)) { $_DATAindividuals->viewList('Individuals_per_reference', $aColsToHide['Individual'], true, true); } print ' </DIV>' . "\n" . ' </DIV>'; $_T->printFooter(); exit; } if ($bImage) { header('Content-type: image/png'); readfile(ROOT_PATH . 'gfx/trans.png'); exit; } define('PAGE_TITLE', 'View data for reference: ' . $aPathElements[1]); $_T->printHeader(); $_T->printTitle(); lovd_showInfoTable('Unknown reference ' . $aPathElements[1], 'stop'); $_T->printFooter();
} // Managers are allowed to download this list... if ($_AUTH['level'] >= LEVEL_MANAGER) { define('FORMAT_ALLOW_TEXTPLAIN', true); } define('PAGE_TITLE', 'View all individuals' . (isset($sGene) ? ' with variants in gene ' . $sGene : '')); $_T->printHeader(); $_T->printTitle(); $aColsToHide = array('panelid', 'diseaseids'); if (isset($sGene)) { $aColsToHide[] = 'genes_screened_'; $aColsToHide[] = 'variants_in_genes_'; } require ROOT_PATH . 'class/object_individuals.php'; $_DATA = new LOVD_Individual(); $_DATA->viewList('Individuals', $aColsToHide, false, false, (bool) ($_AUTH['level'] >= LEVEL_MANAGER), false, true); $_T->printFooter(); exit; } if (PATH_COUNT == 2 && ctype_digit($_PE[1]) && !ACTION) { // URL: /individuals/00000001 // View specific entry. $nID = sprintf('%08d', $_PE[1]); define('PAGE_TITLE', 'View individual #' . $nID); $_T->printHeader(); $_T->printTitle(); // Load appropriate user level for this individual. lovd_isAuthorized('individual', $nID); require ROOT_PATH . 'class/object_individuals.php'; $_DATA = new LOVD_Individual($nID); $zData = $_DATA->viewEntry($nID);
$aNavigation[CURRENT_PATH . '?delete'] = array('cross.png', 'Delete disease entry', 1); } $aNavigation[CURRENT_PATH . '/columns'] = array('menu_columns.png', 'View enabled phenotype columns', 1); $aNavigation[CURRENT_PATH . '/columns?order'] = array('menu_columns.png', 'Re-order enabled phenotype columns', 1); $aNavigation['columns/Phenotype'] = array('menu_columns.png', 'View all available phenotype columns', 1); $aNavigation['phenotypes/disease/' . $nID] = array('menu_magnifying_glass.png', 'View all phenotype entries for this disease', 1); } lovd_showJGNavigation($aNavigation, 'Diseases'); if ($zData['individuals']) { $_GET['search_diseaseids'] = $nID; print '<BR><BR>' . "\n\n"; $_T->printTitle('Individuals', 'H4'); require ROOT_PATH . 'class/object_individuals.php'; $_DATA = new LOVD_Individual(); $_DATA->setSortDefault('id'); $_DATA->viewList('Individuals_for_D_VE', array('panelid', 'diseaseids'), true, false, (bool) ($_AUTH['level'] >= LEVEL_MANAGER), false, true); } $_T->printFooter(); exit; } if (PATH_COUNT == 2 && !ctype_digit($_PE[1]) && !ACTION) { // URL: /diseases/DMD // Try to find a disease by its abbreviation and forward. // When we have multiple hits, refer to listView. $sID = rawurldecode($_PE[1]); $aDiseases = $_DB->query('SELECT id FROM ' . TABLE_DISEASES . ' WHERE symbol = ?', array($sID))->fetchAllColumn(); $n = count($aDiseases); if (!$n) { define('PAGE_TITLE', 'View disease'); $_T->printHeader(); $_T->printTitle();
} else { $zData['saved_work'] = array(); } $_T->printTitle('Individuals', 'H4'); $aUnfinished = !empty($zData['saved_work']['submissions']['individual']) ? array_keys($zData['saved_work']['submissions']['individual']) : array(); if (!empty($aUnfinished)) { require ROOT_PATH . 'class/object_individuals.php'; $_DATA = new LOVD_Individual(); $_GET['search_individualid'] = implode('|', $aUnfinished); $_GET['page_size'] = '10'; if ($_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);