Exemplo n.º 1
0
    }
    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');
$_T->printFooter();
Exemplo n.º 2
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    }
    // Managers are allowed to download this list...
    if ($_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);
Exemplo n.º 3
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            $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();
Exemplo n.º 4
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 } 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);