// URL: /announcements/00001
// View specific entry.
$nID = sprintf('%05d', $_PE[1]);
define('PAGE_TITLE', 'View announcement #' . $nID);
$_T->printHeader();
$_T->printTitle();
// Require manager clearance.
lovd_requireAUTH(LEVEL_MANAGER);
require ROOT_PATH . 'class/object_announcements.php';
$_DATA = new LOVD_Announcement();
$zData = $_DATA->viewEntry($nID);
$aNavigation = array();
// Authorized user is logged in. Provide tools.
$aNavigation[CURRENT_PATH . '?edit'] = array('menu_edit.png', 'Edit announcement', 1);
$aNavigation[CURRENT_PATH . '?delete'] = array('cross.png', 'Delete announcement', 1);
lovd_showJGNavigation($aNavigation, 'Announcements');
$_T->printFooter();
exit;
}
if (PATH_COUNT == 1 && ACTION == 'create') {
// URL: /announcements?create
// URL: /announcements?register
// Create a new announcement.
define('LOG_EVENT', 'AnnouncementCreate');
define('PAGE_TITLE', 'Create a new announcement');
// Require manager clearance.
lovd_requireAUTH(LEVEL_MANAGER);
require ROOT_PATH . 'class/object_announcements.php';
$_DATA = new LOVD_Announcement();
require ROOT_PATH . 'inc-lib-form.php';
if (!empty($_POST)) {
$_DATA = new LOVD_Column();
$zData = $_DATA->viewEntry($sColumnID);
$aTableInfo = lovd_getTableInfoByCategory($zData['category']);
$aNavigation = array();
if ($_AUTH['level'] >= LEVEL_MANAGER || $aTableInfo['shared'] && $_AUTH['level'] >= LEVEL_CURATOR) {
// Authorized user (admin or manager, or curator in case of shared column) is logged in. Provide tools.
// FIXME; needs exact check if there are genes/diseases left that do not have this column.
// A check on 'active' is way too simple and does not work for shared columns.
$aNavigation[CURRENT_PATH . '?add'] = array('menu_plus.png', 'Enable column', !$zData['active'] || $aTableInfo['shared'] ? 1 : 0);
$aNavigation[CURRENT_PATH . '?remove'] = array('cross.png', 'Disable column' . ($aTableInfo['shared'] ? '' : ' and remove values'), $zData['active'] && !$zData['hgvs'] ? 1 : 0);
$aNavigation[CURRENT_PATH . '?delete'] = array('cross.png', 'Delete column', !$zData['active'] && !$zData['hgvs'] && (int) $zData['created_by'] ? 1 : 0);
$aNavigation[CURRENT_PATH . '?edit'] = array('menu_edit.png', 'Edit custom data column settings', $_AUTH['level'] >= LEVEL_MANAGER);
$aNavigation[$_PE[0] . '/' . $zData['category'] . '?order'] = array('menu_columns.png', 'Re-order all ' . $zData['category'] . ' columns', $_AUTH['level'] >= LEVEL_MANAGER);
// $aNavigation[$_SERVER['PHP_SELF'] . '?action=edit_colid&edit_colid=' . rawurlencode($zData['colid'])] = array('menu_edit.png', 'Edit column ID', ($zData['created_by'] && !$bSelected? 1 : 0));
}
lovd_showJGNavigation($aNavigation, 'Columns');
$_T->printFooter();
exit;
}
if (PATH_COUNT == 2 && ACTION == 'order') {
// URL: /columns/Individual?order
// Change in what order the columns will be shown in a viewList/viewEntry.
$sCategory = $_PE[1];
require_once ROOT_PATH . 'inc-lib-columns.php';
$aTableInfo = lovd_getTableInfoByCategory($sCategory);
if (!$aTableInfo) {
$_T->printHeader();
$_T->printTitle('Re-order columns');
lovd_showInfoTable('The specified category does not exist!', 'stop');
$_T->printFooter();
exit;
// Load appropriate user level for this phenotype entry.
lovd_isAuthorized('phenotype', $nID);
require ROOT_PATH . 'class/object_phenotypes.php';
$_DATA = new LOVD_Phenotype('', $nID);
$zData = $_DATA->viewEntry($nID);
$aNavigation = array();
if ($_AUTH && $_AUTH['level'] >= LEVEL_OWNER) {
$aNavigation[CURRENT_PATH . '?edit'] = array('menu_edit.png', 'Edit phenotype information', 1);
if ($zData['statusid'] < STATUS_OK && $_AUTH['level'] >= LEVEL_CURATOR) {
$aNavigation[CURRENT_PATH . '?publish'] = array('check.png', ($zData['statusid'] == STATUS_MARKED ? 'Remove mark from' : 'Publish (curate)') . ' phenotype entry', 1);
}
if ($_AUTH['level'] >= LEVEL_CURATOR) {
$aNavigation[CURRENT_PATH . '?delete'] = array('cross.png', 'Delete phenotype entry', 1);
}
}
lovd_showJGNavigation($aNavigation, 'Phenotypes');
$_T->printFooter();
exit;
}
if (PATH_COUNT == 1 && ACTION == 'create' && !empty($_GET['target']) && ctype_digit($_GET['target'])) {
// URL: /phenotypes?create
// Create a new entry.
// FIXME; ik vind nog steeds dat vooral het begin van deze code nog enigszins rommelig is.
// De structuur van de code voor de controle van de individual ID en het invullen er van,
// is goed af te leiden van transcripts?create.
define('LOG_EVENT', 'PhenotypeCreate');
lovd_requireAUTH(LEVEL_SUBMITTER);
$_GET['target'] = sprintf('%08d', $_GET['target']);
$z = $_DB->query('SELECT id FROM ' . TABLE_INDIVIDUALS . ' WHERE id = ?', array($_GET['target']))->fetchAssoc();
if (!$z) {
define('PAGE_TITLE', 'Create a new phenotype entry');
$nID = sprintf('%08d', $_PE[1]);
define('PAGE_TITLE', 'View transcript #' . $nID);
$_T->printHeader();
$_T->printTitle();
// Load appropriate user level for this transcript.
lovd_isAuthorized('transcript', $nID);
// This call will make database queries if necessary.
require ROOT_PATH . 'class/object_transcripts.php';
$_DATA = new LOVD_Transcript();
$zData = $_DATA->viewEntry($nID);
$aNavigation = array();
if ($_AUTH && $_AUTH['level'] >= LEVEL_CURATOR) {
$aNavigation[CURRENT_PATH . '?edit'] = array('menu_edit.png', 'Edit transcript information', 1);
$aNavigation[CURRENT_PATH . '?delete'] = array('cross.png', 'Delete transcript entry', 1);
}
lovd_showJGNavigation($aNavigation, 'Transcripts');
$_GET['search_transcriptid'] = $nID;
print '<BR><BR>' . "\n\n";
$_T->printTitle('Variants', 'H4');
require ROOT_PATH . 'class/object_transcript_variants.php';
$_DATA = new LOVD_TranscriptVariant($zData['geneid']);
$_DATA->sSortDefault = 'VariantOnTranscript/DNA';
$_DATA->setRowLink('VOT_for_T_VE', 'javascript:window.location.href=\'' . lovd_getInstallURL() . 'variants/{{ID}}#{{transcriptid}}\'; return false');
$_DATA->viewList('VOT_for_T_VE', array('geneid', 'transcriptid', 'id_ncbi', 'id_'));
$_T->printFooter();
exit;
}
if (PATH_COUNT == 2 && !ctype_digit($_PE[1]) && !ACTION) {
// URL: /transcripts/NM_004006.2
// Try to find a transcripts by its NCBI ID and forward.
// When we have multiple hits, refer to listView.
lovd_isAuthorized('screening', $nID);
require ROOT_PATH . 'class/object_screenings.php';
$_DATA = new LOVD_Screening($nID);
$zData = $_DATA->viewEntry($nID);
$aNavigation = array();
if ($_AUTH && $_AUTH['level'] >= LEVEL_OWNER) {
$aNavigation[CURRENT_PATH . '?edit'] = array('menu_edit.png', 'Edit screening information', 1);
if ($zData['variants_found']) {
$aNavigation['variants?create&target=' . $nID] = array('menu_plus.png', 'Add variant to screening', 1);
$aNavigation[CURRENT_PATH . '?removeVariants'] = array('cross.png', 'Remove variants from screening', $zData['variants_found_'] > 0 ? 1 : 0);
}
if ($_AUTH['level'] >= LEVEL_CURATOR) {
$aNavigation[CURRENT_PATH . '?delete'] = array('cross.png', 'Delete screening entry', 1);
}
}
lovd_showJGNavigation($aNavigation, 'Screenings');
if (!empty($zData['search_geneid'])) {
$_GET['search_geneid'] = html_entity_decode(rawurldecode($zData['search_geneid']));
print '<BR><BR>' . "\n\n";
$_T->printTitle('Genes screened', 'H4');
require ROOT_PATH . 'class/object_genes.php';
$_DATA = new LOVD_Gene();
$_DATA->setSortDefault('id');
$_DATA->viewList('Genes_for_S_VE', array(), true, true);
unset($_GET['search_geneid']);
}
if ($zData['variants_found'] || !empty($zData['variants'])) {
$_GET['search_screeningid'] = $nID;
print '<BR><BR>' . "\n\n";
$_T->printTitle('Variants found', 'H4');
require ROOT_PATH . 'class/object_custom_viewlists.php';
$aCol = $_PE;
unset($aCol[0], $aCol[1], $aCol[2]);
// 'diseases/00001/columns';
$sColumnID = implode('/', $aCol);
define('PAGE_TITLE', 'View settings for custom data column ' . $sColumnID . ' for ' . $sUnit . ' #' . $sParentID);
$_T->printHeader();
$_T->printTitle();
// Load appropriate user level for this gene.
lovd_isAuthorized($sUnit, $sParentID);
lovd_requireAUTH(LEVEL_CURATOR);
// Will also stop user if gene given is fake.
require ROOT_PATH . 'class/object_shared_columns.php';
$_DATA = new LOVD_SharedColumn($sParentID, $sCategory . '/' . $sColumnID);
$zData = $_DATA->viewEntry($sCategory . '/' . $sColumnID);
$aNavigation = array(CURRENT_PATH . '?edit' => array('menu_edit.png', 'Edit settings for this ' . $sUnit . ' only', 1), 'columns/' . $sCategory . '/' . $sColumnID . '?remove&target=' . $sParentID => array('cross.png', 'Remove column from this ' . $sUnit, !$zData['hgvs']));
lovd_showJGNavigation($aNavigation, 'ColumnEdit');
$_T->printFooter();
exit;
}
if (PATH_COUNT > 3 && ctype_digit($_PE[1]) && $_PE[2] == 'columns' && ACTION == 'edit') {
// URL: /diseases/00001/columns/IQ?edit
// URL: /diseases/00001/columns/Blood_pressure/Systolic?edit
// View specific enabled column for this disease.
$sUnit = 'disease';
$sCategory = 'Phenotype';
$sParentID = rawurldecode($_PE[1]);
$aCol = $_PE;
unset($aCol[0], $aCol[1], $aCol[2]);
// 'diseases/00001/columns';
$sColumnID = implode('/', $aCol);
define('PAGE_TITLE', 'Edit settings for custom data column ' . $sColumnID . ' for ' . $sUnit . ' #' . $sParentID);
$aNavigation = array();
if ($_AUTH && $_AUTH['level'] >= LEVEL_OWNER) {
$aNavigation[CURRENT_PATH . '?edit'] = array('menu_edit.png', 'Edit individual entry', 1);
if ($zData['statusid'] < STATUS_OK && $_AUTH['level'] >= LEVEL_CURATOR) {
$aNavigation[CURRENT_PATH . '?publish'] = array('check.png', ($zData['statusid'] == STATUS_MARKED ? 'Remove mark from' : 'Publish (curate)') . ' individual entry', 1);
}
// You can only add phenotype information to this individual, when there are phenotype columns enabled.
if ($_DB->query('SELECT COUNT(*) FROM ' . TABLE_IND2DIS . ' AS i2d INNER JOIN ' . TABLE_SHARED_COLS . ' AS sc USING(diseaseid) WHERE i2d.individualid = ?', array($nID))->fetchColumn()) {
$aNavigation['phenotypes?create&target=' . $nID] = array('menu_plus.png', 'Add phenotype information to individual', 1);
}
$aNavigation['screenings?create&target=' . $nID] = array('menu_plus.png', 'Add screening to individual', 1);
if ($_AUTH['level'] >= LEVEL_CURATOR) {
$aNavigation[CURRENT_PATH . '?delete'] = array('cross.png', 'Delete individual entry', 1);
}
}
lovd_showJGNavigation($aNavigation, 'Individuals');
print '<BR><BR>' . "\n\n";
if (!empty($zData['phenotypes'])) {
// List of phenotype entries associated with this person, per disease.
$_GET['search_individualid'] = $nID;
$_T->printTitle('Phenotypes', 'H4');
// Repeat searching for diseases, since this individual might have phenotype entry for a disease he doesn't have.
$zData['diseases'] = $_DB->query('SELECT id, symbol, name FROM ' . TABLE_DISEASES . ' WHERE id IN (?' . str_repeat(', ?', count($zData['phenotypes']) - 1) . ')', $zData['phenotypes'])->fetchAllRow();
require ROOT_PATH . 'class/object_phenotypes.php';
foreach ($zData['diseases'] as $aDisease) {
list($nDiseaseID, $sSymbol, $sName) = $aDisease;
if (in_array($nDiseaseID, $zData['phenotypes'])) {
$_GET['search_diseaseid'] = $nDiseaseID;
$_DATA = new LOVD_Phenotype($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);
// FIXME; this image is actually too small but it doesn't look too bad.
}
$aNavigation[CURRENT_PATH . '?delete'] = array('cross.png', 'Delete user', 1);
$aNavigation['download/all/user/' . $nID] = array('menu_save.png', 'Download all this user\'s data', 1);
} elseif ($_AUTH['id'] == $nID) {
// Viewing himself!
$aNavigation[CURRENT_PATH . '?edit'] = array('menu_edit.png', 'Update your registration', 1);
$aNavigation['download/all/mine'] = array('menu_save.png', 'Download all my data', 1);
} elseif ($_AUTH['level'] >= LEVEL_MANAGER) {
// Managers and up, not viewing own account, not higher level than other user.
$aNavigation['download/all/user/' . $nID] = array('menu_save.png', 'Download all this user\'s data', 1);
}
if ($_AUTH['id'] == $nID || $_AUTH['level'] > $zData['level']) {
$aNavigation[CURRENT_PATH . '?share_access'] = array('', 'Share access to ' . ($_AUTH['id'] == $nID ? 'your' : 'user\'s') . ' entries with other users', 1);
}
lovd_showJGNavigation($aNavigation, 'Users');
if ($_AUTH['level'] >= LEVEL_MANAGER) {
print '<BR><BR>' . "\n\n";
$_T->printTitle('Log entries by this user', 'H4');
require ROOT_PATH . 'class/object_logs.php';
$_DATA = new LOVD_Log();
$_GET['page_size'] = 10;
$_GET['search_userid'] = $nID;
$_DATA->viewList('Logs_for_Users_VE', array('user_', 'del'), true);
}
$_T->printFooter();
exit;
}
if (PATH_COUNT == 1 && in_array(ACTION, array('create', 'register'))) {
// URL: /users?create
// URL: /users?register
// FIXME; For loading the BED file, we'll need a gene symbol!
// $sURLBedFile = rawurlencode(str_replace('https://', 'http://', ($_CONF['location_url']? $_CONF['location_url'] : lovd_getInstallURL())) . 'api/rest/variants/' . $zData['id'] . '?format=text/bed');
// $sURLUCSC = 'http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=Human&db=' . $_CONF['refseq_build'] . '&position=chr' . $zData['chromosome'] . ':' . ($zData['position_g_mrna_start'] - 50) . '-' . ($zData['position_g_mrna_end'] + 50) . ($zData['sense']? '' : '&complement_hg19=1') . '&hgt.customText=' . $sURLBedFile;
// $zData['ucsc'] = 'Show variants in the UCSC Genome Browser (<A href="' . $sURLUCSC . '" target="_blank">full view</A>, <A href="' . $sURLUCSC . rawurlencode('&visibility=4') . '" target="_blank">compact view</A>)';
// // The weird addition in the end is to fake a proper name in Ensembl.
// if ($_CONF['refseq_build'] == 'hg18') {
// $sURLEnsembl = 'http://may2009.archive.ensembl.org/Homo_sapiens/Location/View?r=' . $zData['chromosome'] . ':' . ($zData['position_g_mrna_start'] - 50) . '-' . ($zData['position_g_mrna_end'] + 50) . ';data_URL=' . $sURLBedFile . rawurlencode('&name=/' . $zData['id'] . ' variants');
// //} elseif ($_CONF['refseq_build'] == 'hg19') {
// } else {
// $sURLEnsembl = 'http://www.ensembl.org/Homo_sapiens/Location/View?r=' . $zData['chromosome'] . ':' . ($zData['position_g_mrna_start'] - 50) . '-' . ($zData['position_g_mrna_end'] + 50) . ';contigviewbottom=url:' . $sURLBedFile . rawurlencode('&name=/' . $zData['id'] . ' variants');
// }
// $zData['ensembl'] = 'Show variants in the Ensembl Genome Browser (<A href="' . $sURLEnsembl . '=labels" target="_blank">full view</A>, <A href="' . $sURLEnsembl . '=normal" target="_blank">compact view</A>)';
// $zData['ncbi'] = 'Show distribution histogram of variants in the <A href="http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=' . $_SETT['human_builds'][$_CONF['refseq_build']]['ncbi_sequences'][$zData['chromosome']] . '&v=' . ($zData['position_g_mrna_start'] - 100) . ':' . ($zData['position_g_mrna_end'] + 100) . '&content=7&url=' . $sURLBedFile . '" target="_blank">NCBI Sequence Viewer</A>';
}
}
lovd_showJGNavigation($aNavigation, 'Variants');
print ' <BR><BR>' . "\n\n" . ' <DIV id="viewentryDiv">' . "\n" . ' </DIV>' . "\n\n";
$_GET['search_id_'] = $nID;
print ' <BR><BR>' . "\n\n";
$_T->printTitle('Variant on transcripts', 'H4');
require ROOT_PATH . 'class/object_transcript_variants.php';
$_DATA = new LOVD_TranscriptVariant('', $nID);
$_DATA->setRowID('VOT_for_VOG_VE', 'VOT_{{transcriptid}}');
$_DATA->setRowLink('VOT_for_VOG_VE', 'javascript:window.location.hash = \'{{transcriptid}}\'; return false');
$_DATA->viewList('VOT_for_VOG_VE', array('id_', 'transcriptid', 'status'), true, true);
unset($_GET['search_id_']);
?>
<SCRIPT type="text/javascript">
var prevHash = '';
$( function () {
// URL: /links/001
// View specific entry.
$nID = sprintf('%03d', $_PE[1]);
define('PAGE_TITLE', 'View custom link #' . $nID);
$_T->printHeader();
$_T->printTitle();
// Require manager clearance.
lovd_requireAUTH(LEVEL_MANAGER);
require ROOT_PATH . 'class/object_links.php';
$_DATA = new LOVD_Link();
$zData = $_DATA->viewEntry($nID);
$aNavigation = array();
// Authorized user (admin or manager) is logged in. Provide tools.
$aNavigation[CURRENT_PATH . '?edit'] = array('menu_edit.png', 'Edit custom link', 1);
$aNavigation[CURRENT_PATH . '?delete'] = array('cross.png', 'Delete custom link', 1);
lovd_showJGNavigation($aNavigation, 'Links');
$_T->printFooter();
exit;
}
if (PATH_COUNT == 1 && ACTION == 'create') {
// URL: /links?create
// Create a new entry.
define('PAGE_TITLE', 'Create a new custom link');
define('LOG_EVENT', 'LinkCreate');
// Require manager clearance.
lovd_requireAUTH(LEVEL_MANAGER);
require ROOT_PATH . 'class/object_links.php';
$_DATA = new LOVD_Link();
require ROOT_PATH . 'inc-lib-form.php';
if (!empty($_POST)) {
lovd_errorClean();
