* LOVD is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with LOVD. If not, see <http://www.gnu.org/licenses/>. * *************/ define('ROOT_PATH', './'); require ROOT_PATH . 'inc-init.php'; require ROOT_PATH . 'inc-lib-form.php'; $_T->printHeader(); $_T->printTitle('Uninstall LOVD'); // Require DB admin clearance. lovd_requireAUTH(LEVEL_ADMIN); // If we've gotten this far, we apparently have/had an config, status and user // table. This should suffice to uninstall LOVD even if we don't have a working // installation. // Uninstall lock set? if (isset($_CONF['lock_uninstall']) && $_CONF['lock_uninstall']) { // Sorry, can't remove LOVD... lovd_showInfoTable('Can\'t uninstall LOVD - Uninstall lock in place.', 'warning'); $_T->printFooter(); exit; } if (!empty($_POST)) { lovd_errorClean(); if (!isset($_GET['confirm'])) { // Check password. if (!lovd_verifyPassword($_POST['password'], $_AUTH['password'])) {
print ' <FORM action="' . CURRENT_PATH . '?' . ACTION . '" method="post">' . "\n"; // Array which will make up the form table. $aForm = array_merge($_DATA->getForm(), array(array('', '', 'submit', 'Edit announcement'))); lovd_viewForm($aForm); print '</FORM>' . "\n\n"; $_T->printFooter(); exit; } if (PATH_COUNT == 2 && ctype_digit($_PE[1]) && ACTION == 'delete') { // URL: /announcements/00001?delete // Delete a specific announcement. $nID = sprintf('%05d', $_PE[1]); define('PAGE_TITLE', 'Delete announcement #' . $nID); define('LOG_EVENT', 'AnnouncementDelete'); // Require manager clearance. lovd_requireAUTH(LEVEL_MANAGER); require ROOT_PATH . 'class/object_announcements.php'; $_DATA = new LOVD_Announcement(); $zData = $_DATA->loadEntry($nID); require ROOT_PATH . 'inc-lib-form.php'; 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 ($_POST['password'] && !lovd_verifyPassword($_POST['password'], $_AUTH['password'])) { lovd_errorAdd('password', 'Please enter your correct password for authorization.'); } if (!lovd_error()) {
print(' <DIV id="container"><BR>' . "\n"); // Extra div is to prevent "No entries in the database yet!" error to show up if there are no genes in the database yet. lovd_showInfoTable('Please select a variant you would like to edit', 'information'); $_DATA->viewList($sViewListID, array('id_', 'owned_by_', 'status'), true); print(' </DIV>' . "\n" . ' <SCRIPT type="text/javascript">' . "\n" . ' $("#container").hide();' . "\n" . ' </SCRIPT>' . "\n");*/ $_T->printFooter(); exit; } if (PATH_COUNT == 3 && $_PE[1] == 'review' && ctype_digit($_PE[2]) && !ACTION) { // URL: /submit/review // Review your unfinished submission exit; 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(); lovd_showInfoTable('No such ID!', 'stop'); $_T->printFooter(); exit; } exit; } if (PATH_COUNT == 4 && $_PE[1] == 'finish' && in_array($_PE[2], array('individual', 'screening', 'variant', 'phenotype', 'upload', 'confirmedVariants')) && ctype_digit($_PE[3])) { // URL: /submit/finish/(variant|individual|screening|phenotype|upload|confirmedVariants)/00000001 // URL: /submit/finish/(variant|individual|screening|phenotype)/00000001?edit
$aForm = array_merge($_DATA->getForm(), array(array('', '', 'print', '<INPUT type="submit" value="Edit phenotype information entry">' . ($bSubmit ? ' <INPUT type="submit" value="Cancel" onclick="window.location.href=\'' . lovd_getInstallURL() . 'submit/individual/' . $zData['individualid'] . '\'; return false;" style="border : 1px solid #FF4422;">' : '')))); lovd_viewForm($aForm); print '</FORM>' . "\n\n"; $_T->printFooter(); exit; } if (PATH_COUNT == 2 && ctype_digit($_PE[1]) && ACTION == 'delete') { // URL: /phenotypes/0000000001?delete // Drop specific entry. $nID = sprintf('%010d', $_PE[1]); define('PAGE_TITLE', 'Delete phenotype #' . $nID); define('LOG_EVENT', 'PhenotypeDelete'); // FIXME; hier moet een goede controle komen, wanneer lager is toegestaan. // Load appropriate user level for this phenotype entry. lovd_isAuthorized('phenotype', $nID); lovd_requireAUTH(LEVEL_CURATOR); require ROOT_PATH . 'class/object_phenotypes.php'; $_DATA = new LOVD_Phenotype('', $nID); $zData = $_DATA->loadEntry($nID); require ROOT_PATH . 'inc-lib-form.php'; 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 ($_POST['password'] && !lovd_verifyPassword($_POST['password'], $_AUTH['password'])) { lovd_errorAdd('password', 'Please enter your correct password for authorization.'); } if (!lovd_error()) {
$aHit = array_combine($aHeaders, explode("\"\t\"", trim($sHit, '"'))); print ' <TR class="data" style="cursor : pointer;" onclick="window.open(\'' . htmlspecialchars($aHit['url']) . '\', \'_blank\');">' . "\n" . ' <TD>' . $aHit['hg_build'] . '</TD>' . "\n" . ' <TD>' . $aHit['gene_id'] . '</TD>' . "\n" . ' <TD>' . $aHit['nm_accession'] . '</TD>' . "\n" . ' <TD>' . $aHit['g_position'] . '</TD>' . "\n" . ' <TD>' . $aHit['DNA'] . '</TD>' . "\n" . ' <TD>' . $aHit['variant_id'] . '</TD>' . "\n" . ' <TD>' . substr($aHit['url'], 0, strpos($aHit['url'], '/variants.php')) . '</TD>' . "\n" . ' </TR>' . "\n"; } print '</TABLE>'; $_T->printFooter(); exit; } if (PATH_COUNT == 2 && ctype_digit($_PE[1]) && ACTION == 'map') { // URL: /variants/0000000001?map // Map a variant to additional transcript. $nID = sprintf('%010d', $_PE[1]); define('PAGE_TITLE', 'Map variant entry #' . $nID); define('LOG_EVENT', 'VariantMap'); // Require manager clearance. lovd_isAuthorized('variant', $nID); lovd_requireAUTH(LEVEL_OWNER); require ROOT_PATH . 'class/object_genome_variants.php'; $_DATA = new LOVD_GenomeVariant(); $zData = $_DATA->loadEntry($nID); // Load all transcript ID's that are currently present in the database connected to this variant. $aCurrentTranscripts = $_DB->query('SELECT t.id, t.geneid FROM ' . TABLE_TRANSCRIPTS . ' AS t INNER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot ON (t.id = vot.transcriptid) WHERE vot.id = ? ORDER BY t.geneid', array($nID))->fetchAllCombine(); require ROOT_PATH . 'inc-lib-form.php'; if (POST) { lovd_errorClean(); // Preventing notices... // $_POST['transcripts'] stores the IDs of the transcripts that are supposed to go in TABLE_VARIANTS_ON_TRANSCRIPTS. if (empty($_POST['transcripts']) || !is_array($_POST['transcripts'])) { $_POST['transcripts'] = array(); } else { // Verify all given IDs; they need to exist in the database, and they need to be on the same chromosome. $aTranscripts = $_DB->query('SELECT t.id, t.geneid FROM ' . TABLE_TRANSCRIPTS . ' AS t LEFT OUTER JOIN ' . TABLE_GENES . ' AS g ON (t.geneid = g.id) WHERE g.chromosome = ? AND t.id IN (?' . str_repeat(', ?', count($_POST['transcripts']) - 1) . ')', array_merge(array($zData['chromosome']), $_POST['transcripts']))->fetchAllCombine();