* 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();
