trashCommentInOwner($blogid, $comment['id']);
}
}
}
POD::free($result);
}
if ($result = POD::query("SELECT id, url, site, subject, excerpt FROM {$database['prefix']}RemoteResponses WHERE blogid = {$blogid}")) {
while ($trackback = POD::fetch($result)) {
setProgress($item++ / $items * 100, _t('걸린 글 데이터를 교정하고 있습니다.'));
$correction = '';
if (!Utils_Unicode::validate($trackback['url'])) {
$correction .= ' url = \'' . POD::escapeString(Utils_Unicode::correct($trackback['url'], '?')) . '\'';
}
if (!Utils_Unicode::validate($trackback['site'])) {
$correction .= ' site = \'' . POD::escapeString(Utils_Unicode::correct($trackback['site'], '?')) . '\'';
}
if (!Utils_Unicode::validate($trackback['subject'])) {
$correction .= ' subject = \'' . POD::escapeString(Utils_Unicode::correct($trackback['subject'], '?')) . '\'';
}
if (!Utils_Unicode::validate($trackback['excerpt'])) {
$correction .= ' excerpt = \'' . POD::escapeString(Utils_Unicode::correct($trackback['excerpt'], '?')) . '\'';
}
if (strlen($correction) > 0) {
POD::query("UPDATE {$database['prefix']}RemoteResponses SET {$correction} WHERE blogid = {$blogid} AND id = {$trackback['id']}");
$corrected++;
}
}
POD::free($result);
}
setProgress(100, _t('완료되었습니다.') . "({$corrected})");
finish();
function importer($path, $node, $line)
{
global $blogid, $migrational, $items, $item;
switch ($path) {
case '/blog/setting':
setProgress($item++ / $items * 100, _t('블로그 설정을 복원하고 있습니다.'));
$setting = new BlogSetting();
if (isset($node['title'][0]['.value'])) {
$setting->title = $node['title'][0]['.value'];
}
if (isset($node['description'][0]['.value'])) {
$setting->description = $node['description'][0]['.value'];
}
if (isset($node['banner'][0]['name'][0]['.value'])) {
$setting->banner = $node['banner'][0]['name'][0]['.value'];
}
if (isset($node['useSloganOnPost'][0]['.value'])) {
$setting->useSloganOnPost = $node['useSloganOnPost'][0]['.value'];
}
if (isset($node['postsOnPage'][0]['.value'])) {
$setting->postsOnPage = $node['postsOnPage'][0]['.value'];
}
if (isset($node['postsOnList'][0]['.value'])) {
$setting->postsOnList = $node['postsOnList'][0]['.value'];
}
if (isset($node['postsOnFeed'][0]['.value'])) {
$setting->postsOnFeed = $node['postsOnFeed'][0]['.value'];
}
if (isset($node['publishWholeOnFeed'][0]['.value'])) {
$setting->publishWholeOnFeed = $node['publishWholeOnFeed'][0]['.value'];
}
if (isset($node['acceptGuestComment'][0]['.value'])) {
$setting->acceptGuestComment = $node['acceptGuestComment'][0]['.value'];
}
if (isset($node['acceptcommentOnGuestComment'][0]['.value'])) {
$setting->acceptcommentOnGuestComment = $node['acceptcommentOnGuestComment'][0]['.value'];
}
if (isset($node['language'][0]['.value'])) {
$setting->language = $node['language'][0]['.value'];
}
if (isset($node['timezone'][0]['.value'])) {
$setting->timezone = $node['timezone'][0]['.value'];
}
if (!$setting->save()) {
user_error(__LINE__ . $setting->error);
}
if (!empty($setting->banner) && !empty($node['banner'][0]['content'][0]['.stream'])) {
Attachment::confirmFolder();
Utils_Base64Stream::decode($node['banner'][0]['content'][0]['.stream'], Path::combine(ROOT, 'attach', $blogid, $setting->banner));
Attachment::adjustPermission(Path::combine(ROOT, 'attach', $blogid, $setting->banner));
fclose($node['banner'][0]['content'][0]['.stream']);
unset($node['banner'][0]['content'][0]['.stream']);
}
return true;
case '/blog/category':
setProgress($item++ / $items * 100, _t('분류를 복원하고 있습니다.'));
$category = new Category();
$category->name = $node['name'][0]['.value'];
$category->priority = $node['priority'][0]['.value'];
if (isset($node['root'][0]['.value'])) {
$category->id = 0;
}
if (!$category->add()) {
user_error(__LINE__ . $category->error);
}
if (isset($node['category'])) {
for ($i = 0; $i < count($node['category']); $i++) {
$childCategory = new Category();
$childCategory->parent = $category->id;
$cursor =& $node['category'][$i];
$childCategory->name = $cursor['name'][0]['.value'];
$childCategory->priority = $cursor['priority'][0]['.value'];
if (!$childCategory->add()) {
user_error(__LINE__ . $childCategory->error);
}
}
}
return true;
case '/blog/post':
setProgress($item++ / $items * 100, _t('글을 복원하고 있습니다.'));
$post = new Post();
$post->id = $node['id'][0]['.value'];
$post->slogan = @$node['.attributes']['slogan'];
$post->visibility = $node['visibility'][0]['.value'];
if (isset($node['starred'][0]['.value'])) {
$post->starred = $node['starred'][0]['.value'];
} else {
$post->starred = 0;
}
$post->title = $node['title'][0]['.value'];
$post->content = $node['content'][0]['.value'];
$post->contentformatter = isset($node['content'][0]['.attributes']['formatter']) ? $node['content'][0]['.attributes']['formatter'] : 'ttml';
$post->contenteditor = isset($node['content'][0]['.attributes']['editor']) ? $node['content'][0]['.attributes']['editor'] : 'modern';
$post->location = $node['location'][0]['.value'];
$post->password = isset($node['password'][0]['.value']) ? $node['password'][0]['.value'] : null;
$post->acceptcomment = $node['acceptComment'][0]['.value'];
$post->accepttrackback = $node['acceptTrackback'][0]['.value'];
$post->published = $node['published'][0]['.value'];
if (isset($node['longitude'][0]['.value'])) {
$post->longitude = $node['longitude'][0]['.value'];
}
if (isset($node['latitude'][0]['.value'])) {
$post->latitude = $node['latitude'][0]['.value'];
}
$post->created = @$node['created'][0]['.value'];
$post->modified = @$node['modified'][0]['.value'];
if ($post->visibility == 'private' && intval($post->published) > $_SERVER['REQUEST_TIME'] || !empty($node['appointed'][0]['.value']) && $node['appointed'][0]['.value'] == 'true') {
// for compatibility of appointed entries
$post->visibility = 'appointed';
}
if ($post->slogan == '') {
$post->slogan = 'Untitled' . $post->id;
}
if (!empty($node['category'][0]['.value'])) {
$post->category = Category::getId($node['category'][0]['.value']);
}
if (isset($node['tag'])) {
$post->tags = array();
for ($i = 0; $i < count($node['tag']); $i++) {
if (!empty($node['tag'][$i]['.value'])) {
array_push($post->tags, $node['tag'][$i]['.value']);
}
}
}
if (floatval(Setting::getServiceSettingGlobal('newlineStyle')) >= 1.1 && floatval(@$node['.attributes']['format']) < 1.1) {
$post->content = nl2brWithHTML($post->content);
}
if (!$post->add()) {
user_error(__LINE__ . $post->error);
}
if (isset($node['attachment'])) {
for ($i = 0; $i < count($node['attachment']); $i++) {
$attachment = new Attachment();
$attachment->parent = $post->id;
$cursor =& $node['attachment'][$i];
$attachment->name = $cursor['name'][0]['.value'];
$attachment->label = $cursor['label'][0]['.value'];
$attachment->mime = @$cursor['.attributes']['mime'];
$attachment->size = $cursor['.attributes']['size'];
$attachment->width = $cursor['.attributes']['width'];
$attachment->height = $cursor['.attributes']['height'];
$attachment->enclosure = @$cursor['enclosure'][0]['.value'];
$attachment->attached = $cursor['attached'][0]['.value'];
$attachment->downloads = @$cursor['downloads'][0]['.value'];
if (!$attachment->add()) {
user_error(__LINE__ . $attachment->error);
} else {
if ($cursor['name'][0]['.value'] != $attachment->name) {
$post2 = new Post();
if ($post2->open($post->id, 'id, content')) {
$post2->content = str_replace($cursor['name'][0]['.value'], $attachment->name, $post2->content);
$post2->loadTags();
$post2->update();
$post2->close();
}
unset($post2);
}
}
if (!empty($cursor['content'][0]['.stream'])) {
Utils_Base64Stream::decode($cursor['content'][0]['.stream'], Path::combine(ROOT, 'attach', $blogid, $attachment->name));
Attachment::adjustPermission(Path::combine(ROOT, 'attach', $blogid, $attachment->name));
fclose($cursor['content'][0]['.stream']);
unset($cursor['content'][0]['.stream']);
}
}
}
if (isset($node['comment'])) {
for ($i = 0; $i < count($node['comment']); $i++) {
$comment = new Comment();
$comment->entry = $post->id;
$cursor =& $node['comment'][$i];
$comment->name = $cursor['commenter'][0]['name'][0]['.value'];
if (!empty($cursor['id'][0]['.value'])) {
$comment->id = $cursor['id'][0]['.value'];
}
if (!empty($cursor['commenter'][0]['.attributes']['id'])) {
$comment->commenter = $cursor['commenter'][0]['.attributes']['id'];
}
if (!empty($cursor['commenter'][0]['homepage'][0]['.value'])) {
$comment->homepage = $cursor['commenter'][0]['homepage'][0]['.value'];
}
if (!empty($cursor['commenter'][0]['ip'][0]['.value'])) {
$comment->ip = $cursor['commenter'][0]['ip'][0]['.value'];
}
if (!empty($cursor['commenter'][0]['openid'][0]['.value'])) {
$comment->openid = $cursor['commenter'][0]['openid'][0]['.value'];
}
$comment->password = $cursor['password'][0]['.value'];
$comment->secret = $cursor['secret'][0]['.value'];
$comment->written = $cursor['written'][0]['.value'];
if (isset($cursor['longitude'][0]['.value'])) {
$comment->longitude = $cursor['longitude'][0]['.value'];
}
if (isset($cursor['latitude'][0]['.value'])) {
$comment->latitude = $cursor['latitude'][0]['.value'];
}
$comment->content = $cursor['content'][0]['.value'];
if (!empty($cursor['isFiltered'][0]['.value'])) {
$comment->isfiltered = $cursor['isFiltered'][0]['.value'];
}
if (!$comment->add()) {
user_error(__LINE__ . $comment->error);
}
if (isset($node['comment'][$i]['comment'])) {
for ($j = 0; $j < count($node['comment'][$i]['comment']); $j++) {
$childComment = new Comment();
$childComment->entry = $post->id;
$childComment->parent = $comment->id;
$cursor =& $node['comment'][$i]['comment'][$j];
if (!empty($cursor['id'][0]['.value'])) {
$childComment->id = $cursor['id'][0]['.value'];
}
if (!empty($cursor['commenter'][0]['.attributes']['id'])) {
$childComment->commenter = $cursor['commenter'][0]['.attributes']['id'];
}
$childComment->name = $cursor['commenter'][0]['name'][0]['.value'];
if (!empty($cursor['commenter'][0]['homepage'][0]['.value'])) {
$childComment->homepage = $cursor['commenter'][0]['homepage'][0]['.value'];
}
if (!empty($cursor['commenter'][0]['ip'][0]['.value'])) {
$childComment->ip = $cursor['commenter'][0]['ip'][0]['.value'];
}
if (!empty($cursor['commenter'][0]['openid'][0]['.value'])) {
$childComment->openid = $cursor['commenter'][0]['openid'][0]['.value'];
}
$childComment->password = $cursor['password'][0]['.value'];
$childComment->secret = $cursor['secret'][0]['.value'];
$childComment->written = $cursor['written'][0]['.value'];
if (isset($cursor['longitude'][0]['.value'])) {
$comment->longitude = $cursor['longitude'][0]['.value'];
}
if (isset($cursor['latitude'][0]['.value'])) {
$comment->latitude = $cursor['latitude'][0]['.value'];
}
$childComment->content = $cursor['content'][0]['.value'];
if (!empty($cursor['isFiltered'][0]['.value'])) {
$childComment->isfiltered = $cursor['isFiltered'][0]['.value'];
}
if (!$childComment->add()) {
user_error(__LINE__ . $childComment->error);
}
}
}
}
}
if (isset($node['trackback'])) {
for ($i = 0; $i < count($node['trackback']); $i++) {
$trackback = new Trackback();
$trackback->entry = $post->id;
$cursor =& $node['trackback'][$i];
$trackback->url = $cursor['url'][0]['.value'];
$trackback->site = $cursor['site'][0]['.value'];
$trackback->title = $cursor['title'][0]['.value'];
$trackback->excerpt = @$cursor['excerpt'][0]['.value'];
if (!empty($cursor['ip'][0]['.value'])) {
$trackback->ip = $cursor['ip'][0]['.value'];
}
if (!empty($cursor['received'][0]['.value'])) {
$trackback->received = $cursor['received'][0]['.value'];
}
if (!empty($cursor['isFiltered'][0]['.value'])) {
$trackback->isFiltered = $cursor['isFiltered'][0]['.value'];
}
if (!$trackback->add()) {
user_error(__LINE__ . $trackback->error);
}
}
}
if (isset($node['logs'][0]['trackback'])) {
for ($i = 0; $i < count($node['logs'][0]['trackback']); $i++) {
$log = new TrackbackLog();
$log->entry = $post->id;
$cursor =& $node['logs'][0]['trackback'][$i];
$log->url = $cursor['url'][0]['.value'];
if (!empty($cursor['sent'][0]['.value'])) {
$log->sent = $cursor['sent'][0]['.value'];
}
if (!$log->add()) {
user_error(__LINE__ . $log->error);
}
}
}
return true;
case '/blog/page':
setProgress($item++ / $items * 100, _t('페이지를 복원하고 있습니다.'));
$page = new Page();
$page->id = $node['id'][0]['.value'];
$page->slogan = @$node['.attributes']['slogan'];
$page->visibility = $node['visibility'][0]['.value'];
if (isset($node['starred'][0]['.value'])) {
$page->starred = $node['starred'][0]['.value'];
} else {
$page->starred = 0;
}
$page->title = $node['title'][0]['.value'];
$page->content = $node['content'][0]['.value'];
$page->contentformatter = isset($node['content']['.attributes']['formatter']) ? $node['content']['.attributes']['formatter'] : getDefaultFormatter();
$page->contenteditor = isset($node['content']['.attributes']['editor']) ? $node['content']['.attributes']['editor'] : getDefaultEditor();
$page->published = $node['published'][0]['.value'];
$page->created = @$node['created'][0]['.value'];
$page->modified = @$node['modified'][0]['.value'];
if (floatval(Setting::getServiceSettingGlobal('newlineStyle')) >= 1.1 && floatval(@$node['.attributes']['format']) < 1.1) {
$page->content = nl2brWithHTML($page->content);
}
if (!$page->add()) {
user_error(__LINE__ . $page->error);
}
if (isset($node['attachment'])) {
for ($i = 0; $i < count($node['attachment']); $i++) {
$attachment = new Attachment();
$attachment->parent = $page->id;
$cursor =& $node['attachment'][$i];
$attachment->name = $cursor['name'][0]['.value'];
$attachment->label = $cursor['label'][0]['.value'];
$attachment->mime = @$cursor['.attributes']['mime'];
$attachment->size = $cursor['.attributes']['size'];
$attachment->width = $cursor['.attributes']['width'];
$attachment->height = $cursor['.attributes']['height'];
$attachment->enclosure = @$cursor['enclosure'][0]['.value'];
$attachment->attached = $cursor['attached'][0]['.value'];
$attachment->downloads = @$cursor['downloads'][0]['.value'];
if (Attachment::doesExist($attachment->name)) {
if (!$attachment->add()) {
user_error(__LINE__ . $attachment->error);
}
$page2 = new Page();
if ($page2->open($page->id, 'id, content')) {
$page2->content = str_replace($cursor['name'][0]['.value'], $attachment->name, $page2->content);
$page2->update();
$page2->close();
}
unset($page2);
} else {
if (!$attachment->add()) {
user_error(__LINE__ . $attachment->error);
}
}
if (!empty($cursor['content'][0]['.stream'])) {
Utils_Base64Stream::decode($cursor['content'][0]['.stream'], Path::combine(ROOT, 'attach', $blogid, $attachment->name));
Attachment::adjustPermission(Path::combine(ROOT, 'attach', $blogid, $attachment->name));
fclose($cursor['content'][0]['.stream']);
unset($cursor['content'][0]['.stream']);
}
}
}
return true;
case '/blog/notice':
setProgress($item++ / $items * 100, _t('공지를 복원하고 있습니다.'));
$notice = new Notice();
$notice->id = $node['id'][0]['.value'];
$notice->slogan = @$node['.attributes']['slogan'];
$notice->visibility = $node['visibility'][0]['.value'];
if (isset($node['starred'][0]['.value'])) {
$notice->starred = $node['starred'][0]['.value'];
} else {
$notice->starred = 0;
}
$notice->title = $node['title'][0]['.value'];
$notice->content = $node['content'][0]['.value'];
$notice->contentformatter = isset($node['content'][0]['.attributes']['formatter']) ? $node['content'][0]['.attributes']['formatter'] : getDefaultFormatter();
$notice->contenteditor = isset($node['content'][0]['.attributes']['editor']) ? $node['content'][0]['.attributes']['editor'] : getDefaultEditor();
$notice->published = intval($node['published'][0]['.value']);
$notice->created = @$node['created'][0]['.value'];
$notice->modified = @$node['modified'][0]['.value'];
if (floatval(Setting::getServiceSettingGlobal('newlineStyle')) >= 1.1 && floatval(@$node['.attributes']['format']) < 1.1) {
$notice->content = nl2brWithHTML($notice->content);
}
if (!$notice->add()) {
user_error(__LINE__ . $notice->error);
}
if (isset($node['attachment'])) {
for ($i = 0; $i < count($node['attachment']); $i++) {
$attachment = new Attachment();
$attachment->parent = $notice->id;
$cursor =& $node['attachment'][$i];
$attachment->name = $cursor['name'][0]['.value'];
$attachment->label = $cursor['label'][0]['.value'];
$attachment->mime = @$cursor['.attributes']['mime'];
$attachment->size = $cursor['.attributes']['size'];
$attachment->width = $cursor['.attributes']['width'];
$attachment->height = $cursor['.attributes']['height'];
$attachment->enclosure = @$cursor['enclosure'][0]['.value'];
$attachment->attached = $cursor['attached'][0]['.value'];
$attachment->downloads = @$cursor['downloads'][0]['.value'];
if (Attachment::doesExist($attachment->name)) {
if (!$attachment->add()) {
user_error(__LINE__ . $attachment->error);
}
$notice2 = new Notice();
if ($notice2->open($notice->id, 'id, content')) {
$notice2->content = str_replace($cursor['name'][0]['.value'], $attachment->name, $notice2->content);
$notice2->update();
$notice2->close();
}
unset($notice2);
} else {
if (!$attachment->add()) {
user_error(__LINE__ . $attachment->error);
}
}
if (!empty($cursor['content'][0]['.stream'])) {
Utils_Base64Stream::decode($cursor['content'][0]['.stream'], Path::combine(ROOT, 'attach', $blogid, $attachment->name));
Attachment::adjustPermission(Path::combine(ROOT, 'attach', $blogid, $attachment->name));
fclose($cursor['content'][0]['.stream']);
unset($cursor['content'][0]['.stream']);
}
}
}
return true;
case '/blog/keyword':
setProgress($item++ / $items * 100, _t('키워드를 복원하고 있습니다.'));
$keyword = new Keyword();
$keyword->id = $node['id'][0]['.value'];
$keyword->visibility = $node['visibility'][0]['.value'];
if (isset($node['starred'][0]['.value'])) {
$keyword->starred = $node['starred'][0]['.value'];
} else {
$keyword->starred = 0;
}
$keyword->name = $node['name'][0]['.value'];
$keyword->description = $node['description'][0]['.value'];
$keyword->descriptionEditor = isset($node['description'][0]['.attributes']['editor']) ? $node['description'][0]['.attributes']['editor'] : getDefaultEditor();
$keyword->descriptionFormatter = isset($node['description'][0]['.attributes']['formatter']) ? $node['description'][0]['.attributes']['formatter'] : getDefaultFormatter();
$keyword->published = intval($node['published'][0]['.value']);
$keyword->created = @$node['created'][0]['.value'];
$keyword->modified = @$node['modified'][0]['.value'];
if (floatval(Setting::getServiceSettingGlobal('newlineStyle')) >= 1.1 && floatval(@$node['.attributes']['format']) < 1.1) {
$keyword->description = nl2brWithHTML($keyword->description);
}
if (!$keyword->add()) {
user_error(__LINE__ . $keyword->error);
}
if (isset($node['attachment'])) {
for ($i = 0; $i < count($node['attachment']); $i++) {
$attachment = new Attachment();
$attachment->parent = $keyword->id;
$cursor =& $node['attachment'][$i];
$attachment->name = $cursor['name'][0]['.value'];
$attachment->label = $cursor['label'][0]['.value'];
$attachment->mime = @$cursor['.attributes']['mime'];
$attachment->size = $cursor['.attributes']['size'];
$attachment->width = $cursor['.attributes']['width'];
$attachment->height = $cursor['.attributes']['height'];
$attachment->enclosure = @$cursor['enclosure'][0]['.value'];
$attachment->attached = $cursor['attached'][0]['.value'];
$attachment->downloads = @$cursor['downloads'][0]['.value'];
if (Attachment::doesExist($attachment->name)) {
if (!$attachment->add()) {
user_error(__LINE__ . $attachment->error);
}
$keyword2 = new Keyword();
if ($keyword2->open($keyword->id, 'id, content')) {
$keyword2->content = str_replace($cursor['name'][0]['.value'], $attachment->name, $keyword2->content);
$keyword2->update();
$keyword2->close();
}
unset($keyword2);
} else {
if (!$attachment->add()) {
user_error(__LINE__ . $attachment->error);
}
}
if (!empty($cursor['content'][0]['.stream'])) {
Utils_Base64Stream::decode($cursor['content'][0]['.stream'], Path::combine(ROOT, 'attach', $blogid, $attachment->name));
Attachment::adjustPermission(Path::combine(ROOT, 'attach', $blogid, $attachment->name));
fclose($cursor['content'][0]['.stream']);
unset($cursor['content'][0]['.stream']);
}
}
}
return true;
case '/blog/linkCategories':
setProgress($item++ / $items * 100, _t('링크 카테고리를 복원하고 있습니다.'));
$linkCategory = new LinkCategories();
$linkCategory->name = $node['name'][0]['.value'];
$linkCategory->priority = $node['priority'][0]['.value'];
$linkCategory->visibility = !isset($node['visibility'][0]['.value']) || empty($node['visibility'][0]['.value']) ? 2 : $node['visibility'][0]['.value'];
$linkCategory->id = LinkCategories::getId($linkCategory->name);
if ($linkCategory->id) {
if (!$linkCategory->update()) {
user_error(__LINE__ . $linkCategory->error);
}
} else {
if (!$linkCategory->add()) {
user_error(__LINE__ . $linkCategory->error);
}
}
return true;
case '/blog/link':
setProgress($item++ / $items * 100, _t('링크를 복원하고 있습니다.'));
$link = new Link();
$link->category = empty($node['category'][0]['.value']) ? 0 : $node['category'][0]['.value'];
$link->url = $node['url'][0]['.value'];
$link->title = $node['title'][0]['.value'];
if (!empty($node['feed'][0]['.value'])) {
$link->feed = $node['feed'][0]['.value'];
}
if (!empty($node['registered'][0]['.value'])) {
$link->registered = $node['registered'][0]['.value'];
}
if (!empty($node['xfn'][0]['.value'])) {
$link->xfn = $node['xfn'][0]['.value'];
}
$link->id = Link::getId($link->url);
if ($link->id) {
if (!$link->update()) {
user_error(__LINE__ . $link->error);
}
} else {
if (!$link->add()) {
user_error(__LINE__ . $link->error);
}
}
return true;
case '/blog/logs/referer':
setProgress($item++ / $items * 100, _t('리퍼러 로그를 복원하고 있습니다.'));
$log = new RefererLog();
if (isset($node['path'][0]['.value'])) {
$log->url = $node['path'][0]['.value'];
} else {
$log->url = $node['url'][0]['.value'];
}
$log->referred = $node['referred'][0]['.value'];
if (!$log->add(false)) {
user_error(__LINE__ . $log->error);
}
return true;
case '/blog/commentsNotified/comment':
setProgress($item++ / $items * 100, _t('댓글 알리미 내용을 복원하고 있습니다.'));
$cmtNotified = new CommentNotified();
$cmtNotified->id = $node['id'][0]['.value'];
$cursor =& $node['commenter'][0];
$cmtNotified->name = $cursor['name'][0]['.value'];
$cmtNotified->homepage = $cursor['homepage'][0]['.value'];
$cmtNotified->ip = $cursor['ip'][0]['.value'];
$cmtNotified->entry = $node['entry'][0]['.value'];
$cmtNotified->password = $node['password'][0]['.value'];
$cmtNotified->content = $node['content'][0]['.value'];
$cmtNotified->parent = $node['parent'][0]['.value'];
$cmtNotified->secret = $node['secret'][0]['.value'];
$cmtNotified->written = $node['written'][0]['.value'];
$cmtNotified->modified = $node['modified'][0]['.value'];
$cmtNotified->url = $node['url'][0]['.value'];
$cmtNotified->isnew = $node['isNew'][0]['.value'];
$site = new CommentNotifiedSiteInfo();
if (!$site->open("url = '{$node['site'][0]['.value']}'")) {
$site->title = '';
$site->name = '';
$site->modified = 31536000;
$site->url = $node['site'][0]['.value'];
$site->add();
}
$cmtNotified->siteid = $site->id;
$site->close();
$cmtNotified->remoteid = $node['remoteId'][0]['.value'];
$cmtNotified->entrytitle = !isset($node['entryTitle'][0]['.value']) || empty($node['entryTitle'][0]['.value']) ? 'No title' : $node['entryTitle'][0]['.value'];
$cmtNotified->entryurl = $node['entryUrl'][0]['.value'];
if (!$cmtNotified->add()) {
user_error(__LINE__ . $cmtNotified->error);
}
return true;
case '/blog/commentsNotifiedSiteInfo/site':
setProgress($item++ / $items * 100, _t('댓글 알리미 내용을 복원하고 있습니다.'));
$cmtNotifiedSite = new CommentNotifiedSiteInfo();
if ($cmtNotifiedSite->open("url = '{$node['url'][0]['.value']}'")) {
if (intval($node['modified'][0]['.value']) > intval($cmtNotifiedSite->modified)) {
$cmtNotifiedSite->title = $node['title'][0]['.value'];
$cmtNotifiedSite->name = $node['name'][0]['.value'];
$cmtNotifiedSite->modified = $node['modified'][0]['.value'];
}
if (!$cmtNotifiedSite->update()) {
user_error(__LINE__ . $cmtNotifiedSite->error);
}
} else {
$cmtNotifiedSite->url = $node['url'][0]['.value'];
$cmtNotifiedSite->title = $node['title'][0]['.value'];
$cmtNotifiedSite->name = $node['name'][0]['.value'];
$cmtNotifiedSite->modified = $node['modified'][0]['.value'];
if (!$cmtNotifiedSite->add()) {
user_error(__LINE__ . $cmtNotifiedSite->error);
}
}
return true;
case '/blog/statistics/referer':
setProgress($item++ / $items * 100, _t('리퍼러 통계를 복원하고 있습니다.'));
$statistics = new RefererStatistics();
$statistics->host = $node['host'][0]['.value'];
$statistics->count = $node['count'][0]['.value'];
if (!$statistics->add()) {
user_error(__LINE__ . $statistics->error);
}
return true;
case '/blog/statistics/visits':
setProgress($item++ / $items * 100, _t('블로그 통계 정보를 복원하고 있습니다.'));
$statistics = new BlogStatistics();
$statistics->visits = $node['.value'];
if (!$statistics->add()) {
user_error(__LINE__ . $statistics->error);
}
return true;
case '/blog/statistics/daily':
setProgress($item++ / $items * 100, _t('일별 통계 정보를 복원하고 있습니다.'));
$statistics = new DailyStatistics();
$statistics->date = $node['date'][0]['.value'];
$statistics->visits = $node['visits'][0]['.value'];
if (!$statistics->add()) {
user_error(__LINE__ . $statistics->error);
}
return true;
case '/blog/skin':
setProgress($item++ / $items * 100, _t('스킨 설정을 복원하고 있습니다.'));
$setting = new SkinSetting();
if (false) {
$setting->skin = $node['name'][0]['.value'];
if (!$setting->save()) {
user_error(__LINE__ . $setting->error);
}
$setting->skin = null;
}
$setting->entriesOnRecent = $node['entriesOnRecent'][0]['.value'];
$setting->commentsOnRecent = $node['commentsOnRecent'][0]['.value'];
$setting->trackbacksOnRecent = $node['trackbacksOnRecent'][0]['.value'];
$setting->commentsOnGuestbook = $node['commentsOnGuestbook'][0]['.value'];
$setting->tagsOnTagbox = $node['tagsOnTagbox'][0]['.value'];
$setting->alignOnTagbox = $node['alignOnTagbox'][0]['.value'];
$setting->expandComment = $node['expandComment'][0]['.value'];
$setting->expandTrackback = $node['expandTrackback'][0]['.value'];
if (!empty($node['recentNoticeLength'][0]['.value'])) {
$setting->recentNoticeLength = $node['recentNoticeLength'][0]['.value'];
}
$setting->recentEntryLength = $node['recentEntryLength'][0]['.value'];
$setting->recentTrackbackLength = $node['recentTrackbackLength'][0]['.value'];
$setting->linkLength = $node['linkLength'][0]['.value'];
$setting->showListOnCategory = $node['showListOnCategory'][0]['.value'];
$setting->showListOnArchive = $node['showListOnArchive'][0]['.value'];
if (isset($node['tree'])) {
$cursor =& $node['tree'][0];
$setting->tree = $cursor['name'][0]['.value'];
$setting->colorOnTree = $cursor['color'][0]['.value'];
$setting->bgcolorOnTree = $cursor['bgColor'][0]['.value'];
$setting->activecolorOnTree = $cursor['activeColor'][0]['.value'];
$setting->activebgcolorOnTree = $cursor['activeBgColor'][0]['.value'];
$setting->labelLengthOnTree = $cursor['labelLength'][0]['.value'];
$setting->showValueOnTree = $cursor['showValue'][0]['.value'];
}
if (!$setting->save()) {
user_error(__LINE__ . $setting->error);
}
return true;
case '/blog/plugin':
// setProgress($item++ / $items * 100, _t('플러그인 설정을 복원하고 있습니다.'));
// $setting = new PluginSetting();
// $setting->name = $node['name'][0]['.value'];
// $setting->setting = $node['setting'][0]['.value'];
// if (!$setting->add())
// user_error(__LINE__ . $setting->error);
return true;
case '/blog/personalization':
// setProgress($item++ / $items * 100, _t('사용자 편의 설정을 복원하고 있습니다.'));
// $setting = new UserSetting();
// $setting->name = 'rowsPerPage';
// $setting->value = $node['rowsPerPage'][0]['.value'];
// if (!$setting->add())
// user_error(__LINE__ . $setting->error);
// $setting->name = 'readerPannelVisibility';
// $setting->value = $node['readerPannelVisibility'][0]['.value'];
// if (!$setting->add())
// user_error(__LINE__ . $setting->error);
// $setting->name = 'readerPannelHeight';
// $setting->value = $node['readerPannelHeight'][0]['.value'];
// if (!$setting->add())
// user_error(__LINE__ . $setting->error);
// $setting->name = 'lastVisitNotifiedPage';
// $setting->value = $node['lastVisitNotifiedPage'][0]['.value'];
// if (!$setting->add())
// user_error(__LINE__ . $setting->error);
return true;
case '/blog/userSetting':
// setProgress($item++ / $items * 100, _t('사용자 편의 설정을 복원하고 있습니다'));
// $setting = new UserSetting();
// $setting->name = $node['name'][0]['.value'];
// $setting->value = $node['value'][0]['.value'];
// if (!$setting->add())
// user_error(__LINE__ . $setting->error);
return true;
case '/blog/guestbook/comment':
setProgress($item++ / $items * 100, _t('방명록을 복원하고 있습니다.'));
$comment = new GuestComment();
$comment->name = $node['commenter'][0]['name'][0]['.value'];
if (!empty($node['id'][0]['.value'])) {
$comment->id = $node['id'][0]['.value'];
}
if (!empty($node['commenter'][0]['.attributes']['id'])) {
$comment->commenter = $node['commenter'][0]['.attributes']['id'];
}
if (!empty($node['commenter'][0]['homepage'][0]['.value'])) {
$comment->homepage = $node['commenter'][0]['homepage'][0]['.value'];
}
if (!empty($node['commenter'][0]['ip'][0]['.value'])) {
$comment->ip = $node['commenter'][0]['ip'][0]['.value'];
}
if (!empty($node['commenter'][0]['openid'][0]['.value'])) {
$comment->openid = $node['commenter'][0]['openid'][0]['.value'];
}
$comment->password = $node['password'][0]['.value'];
$comment->secret = @$node['secret'][0]['.value'];
$comment->written = $node['written'][0]['.value'];
$comment->content = $node['content'][0]['.value'];
if (!$comment->add()) {
user_error(__LINE__ . $comment->error);
}
if (isset($node['comment'])) {
for ($j = 0; $j < count($node['comment']); $j++) {
$childComment = new GuestComment();
$childComment->parent = $comment->id;
$cursor =& $node['comment'][$j];
$childComment->name = $cursor['commenter'][0]['name'][0]['.value'];
if (!empty($cursor['id'][0]['.value'])) {
$comment->id = $cursor['id'][0]['.value'];
}
if (!empty($cursor['commenter'][0]['.attributes']['id'])) {
$childComment->commenter = $cursor['commenter'][0]['.attributes']['id'];
}
if (!empty($cursor['commenter'][0]['homepage'][0]['.value'])) {
$childComment->homepage = $cursor['commenter'][0]['homepage'][0]['.value'];
}
if (!empty($cursor['commenter'][0]['ip'][0]['.value'])) {
$childComment->ip = $cursor['commenter'][0]['ip'][0]['.value'];
}
if (!empty($cursor['commenter'][0]['openid'][0]['.value'])) {
$childComment->openid = $cursor['commenter'][0]['openid'][0]['.value'];
}
$childComment->password = $cursor['password'][0]['.value'];
$childComment->secret = @$cursor['secret'][0]['.value'];
$childComment->written = $cursor['written'][0]['.value'];
$childComment->content = $cursor['content'][0]['.value'];
if (!$childComment->add()) {
user_error(__LINE__ . $childComment->error);
}
}
}
return true;
case '/blog/filter':
setProgress($item++ / $items * 100, _t('필터 설정을 복원하고 있습니다.'));
$filter = new Filter();
$filter->type = $node['.attributes']['type'];
$filter->pattern = $node['pattern'][0]['.value'];
if (!$filter->add()) {
user_error(__LINE__ . $filter->error);
}
return true;
case '/blog/feed':
setProgress($item++ / $items * 100, _t('리더 데이터를 복원하고 있습니다.'));
$feed = new Feed();
if (!empty($node['group'][0]['.value'])) {
$feed->group = FeedGroup::getId($node['group'][0]['.value'], true);
}
$feed->url = $node['url'][0]['.value'];
if (!$feed->add()) {
user_error(__LINE__ . $feed->error);
}
return true;
case '/blog/line':
setProgress($item++ / $items * 100, _t('라인을 복원하고 있습니다.'));
$line = Model_Line::getInstance();
$line->reset();
if (!empty($node['author'][0]['.value'])) {
$line->author = $node['author'][0]['.value'];
}
if (!empty($node['category'][0]['.value'])) {
$line->category = $node['category'][0]['.value'];
}
if (!empty($node['root'][0]['.value'])) {
$line->root = $node['root'][0]['.value'];
}
if (!empty($node['permalink'][0]['.value'])) {
$line->permalink = $node['permalink'][0]['.value'];
}
if (!empty($node['content'][0]['.value'])) {
$line->content = $node['content'][0]['.value'];
}
if (!empty($node['created'][0]['.value'])) {
$line->created = intval($node['created'][0]['.value']);
}
if ($line->add()) {
return true;
} else {
user_error(__LINE__ . $line->_error);
}
}
}
# MAIN - the beginning of execution for this page
############################################################################
$modelID = $_SESSION['bgjob']['modelID'];
$model = $_SESSION['models'][$modelID];
$pdbDir = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS;
$pdb = $pdbDir . '/' . $model['pdb'];
// Set up progress message
$tasks['convert'] = "Convert pdb with <code>remediator -oldout</code>";
$tasks['notebook'] = "Add entry to lab notebook";
setProgress($tasks, 'convert');
// updates the progress display if running as a background job
if (!file_exists($pdbDir)) {
mkdir($pdbDir, 0777);
}
// shouldn't ever happen, but might...
$outpdb = $pdbDir . '/' . $modelID . "v23.pdb";
downgradePDB($pdb, $outpdb);
setProgress($tasks, 'notebook');
$outpdburl = $_SESSION['dataURL'] . '/' . MP_DIR_MODELS . '/' . $modelID . "v23.pdb";
$entry = "remediator was run on {$model['pdb']} to convert its atoms to PDB v2.3 format.\n";
$entry .= "<p>You can now <a href='{$outpdburl}'>download the converted PDB file with hydrogens</a> ";
$entry .= "or <a href='download_trimmed.php?{$_SESSION['sessTag']}&file={$outpdb}'>without hydrogens</a>.</p>\n";
$entry .= $pdbEntries;
//$entry .= "<p>A kinemage of all of the fragments is ready for viewing in KiNG: ".linkKinemage($modelID.'.kin')."</p>\n";
$_SESSION['bgjob']['labbookEntry'] = addLabbookEntry("Converted {$model['pdb']} to {$modelID}" . "v23.pdb.", $entry, "{$modelID}|{$newModel['id']}", "auto", "downgrade.gif");
setProgress($tasks, null);
############################################################################
// Clean up and go home
unset($_SESSION['bgjob']['processID']);
$_SESSION['bgjob']['endTime'] = time();
$_SESSION['bgjob']['isRunning'] = false;
}
$sql = "SELECT * FROM computers_deploy_tasks WHERE task_type=1 AND status=1";
$q = new mysql();
$q = new mysql();
$results = $q->QUERY_SQL($sql, "artica_backup");
while ($ligne = @mysql_fetch_array($results, MYSQL_ASSOC)) {
$GLOBALS[__FILE__]["TASKID"] = $ligne["ID"];
$GLOBALS[__FILE__]["storage_id"] = $ligne["storage_id"];
$GLOBALS[__FILE__]["group_id"] = $ligne["group_id"];
echo "Find {$GLOBALS[__FILE__]["TASKID"]} task id\n";
if (EXPLODE_COMPUTERS()) {
setStatus(2);
setProgress(1);
} else {
setStatus(-1);
setProgress(0);
}
}
ScanComputers();
function setProgress($pource)
{
$sql = "UPDATE computers_deploy_tasks SET progress={$pource} WHERE ID={$GLOBALS[__FILE__]["TASKID"]}";
$q = new mysql();
$q->QUERY_SQL($sql, "artica_backup");
if (!$q->ok) {
echo "{$sql} {$q->mysql_error}\n";
}
}
function setStatus($status)
{
$sql = "UPDATE computers_deploy_tasks SET status={$status} WHERE ID={$GLOBALS[__FILE__]["TASKID"]}";
function removeHydrogens($inpath, $outpath)
{
$tasks = getProgressTasks();
$tasks['reducetrim'] = "Remove hydrogens to avoid possible conflict with hydrogen lengths";
$tmp1 = mpTempfile("tmp_pdb_");
setProgress($tasks, 'reducetrim');
reduceTrim($inpath, $tmp1);
copy($tmp1, $outpath);
// Clean up temp files
unlink($tmp1);
setProgress($tasks, null);
// all done
}
/**
* This is the uber-validation function that calls everything below.
* It is suited for use from either the web or command line interface.
* This only makes sense in terms of an active session.
* modelID ID code for model to process
* opts has the following keys mapped to boolean flags:
* doKinemage make the multi-criterion kinemage at all?
* kinClashes show clash dots?
* kinHbonds show H-bond dots?
* kinContacts show contact dots?
* kinRama show Rama outliers?
* kinRota show rotamer outliers?
* kinGeom show bond length and angle outliers?
* kinCBdev show C-beta deviations?
* kinBaseP show base-phosphate perpendiculars?
* kinSuite show RNA backbone conformational outliers?
* kinAltConfs show alternate conformations?
* kinBfactor show B-factor color model?
* kinOccupancy show occupancy color model?
* kinRibbons show ribbons?
* kinForceViews force running clashlist, etc to provide @views of bad spots?
* doCharts make the multi-criterion chart and other plots/tables/lists?
* chartClashlist run clashlistcluster?
* chartRama do Rama plots and analysis?
* chartRota do rotamer analysis?
* chartGeom do bond length and angle outliers?
* chartCBdev do CB dev plots and analysis?
* chartBaseP check base-phosphate perpendiculars?
* chartSuite check RNA backbone conformations?
* chartHoriz do horizontal chart?
* chartCoot do coot chart?
* chartMulti do html multi chart?
* chartNotJustOut include residues that have no problems in the list?
* chartAltloc remove redundant residue rows when altlocs present?
* chartImprove compare to reduce -(no)build results to show improvement?
*
* This function returns some HTML suitable for using in a lab notebook entry.
*/
function runAnalysis($modelID, $opts)
{
//{{{ Set up file/directory vars and the task list
// If doKinemage or doCharts is off, turn off all their subordinates
if (!$opts['doKinemage']) {
foreach ($opts as $k => $v) {
if (startsWith($k, 'kin')) {
$opts[$k] = false;
}
}
}
if (!$opts['doCharts']) {
foreach ($opts as $k => $v) {
if (startsWith($k, 'chart')) {
$opts[$k] = false;
}
}
}
if ($opts['kinForceViews']) {
foreach ($opts as $k => $v) {
if (startsWith($k, 'chart')) {
$opts[$k] = true;
}
}
}
$model = $_SESSION['models'][$modelID];
$modelDir = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS;
$modelURL = $_SESSION['dataURL'] . '/' . MP_DIR_MODELS;
$kinDir = $_SESSION['dataDir'] . '/' . MP_DIR_KINS;
$kinURL = $_SESSION['dataURL'] . '/' . MP_DIR_KINS;
if (!file_exists($kinDir)) {
mkdir($kinDir, 0777);
}
$rawDir = $_SESSION['dataDir'] . '/' . MP_DIR_RAWDATA;
if (!file_exists($rawDir)) {
mkdir($rawDir, 0777);
}
$chartDir = $_SESSION['dataDir'] . '/' . MP_DIR_CHARTS;
$chartURL = $_SESSION['dataURL'] . '/' . MP_DIR_CHARTS;
if (!file_exists($chartDir)) {
mkdir($chartDir, 0777);
}
$xrayDir = $_SESSION['dataDir'] . '/' . MP_DIR_XRAYDATA;
$infile = "{$modelDir}/{$model['pdb']}";
$reduce_blength = $_SESSION['reduce_blength'];
if (isset($model['mtz_file'])) {
$mtz_file = $model['mtz_file'];
} else {
$mtz_file = $_SESSION['models'][$model['parent']]['mtz_file'];
}
if ($opts['chartRama']) {
$tasks['rama'] = "Do Ramachandran analysis and make plots (<code>ramalyze</code>)";
}
if ($opts['chartRota']) {
$tasks['rota'] = "Do rotamer analysis (<code>rotalyze</code>)";
}
if ($opts['chartCBdev']) {
$tasks['cbeta'] = "Do Cβ deviation analysis and make kins (<code>cbetadev</code>)";
}
if ($opts['chartOmega']) {
$tasks['omega'] = "Do cis-peptide analysis (<code>omegalyze</code>)";
}
if ($opts['chartCablamLow']) {
$tasks['cablam'] = "Do CaBLAM analysis (<code>cablam_validate</code>)";
}
if ($opts['chartBaseP']) {
$tasks['base-phos'] = "Do RNA sugar pucker analysis";
}
if ($opts['chartSuite']) {
$tasks['suitename'] = "Do RNA backbone conformations analysis";
}
if ($model['stats']['use_cdl']) {
$geomsg = "Using CDL";
} else {
$geomsg = "";
}
if ($opts['chartGeom']) {
$tasks['geomValidation'] = "Do bond length and angle geometry analysis (<code>mp_geo</code>) {$geomsg}";
}
if ($opts['chartClashlist']) {
$tasks['clashlist'] = "Run <code>clashscore</code> to find bad clashes and clashscore";
}
if ($opts['chartImprove']) {
$tasks['improve'] = "Suggest / report on fixes";
}
if ($opts['doCharts'] && !$opts['chartMulti']) {
$tasks['chartsummary'] = "Create summary chart";
}
if ($opts['chartMulti']) {
$tasks['multichart'] = "Create multi-criterion chart";
}
if ($opts['chartHoriz']) {
$tasks['runRSCC'] = "Run real-space correlation";
$tasks['charthoriz'] = "Create horizontal RSCC chart";
}
if ($opts['chartCoot']) {
$tasks['cootchart'] = "Create chart for use in Coot";
}
if ($opts['doKinemage']) {
$tasks['multikin'] = "Create multi-criterion kinemage";
}
//if($opts['doLowRes']) $tasks['lowResKin'] = "Create low-resolution multi-criterion kinemage";
//$doRem40 = $opts['chartClashlist'] || $opts['chartRama'] || $opts['chartRota'];
//if($doRem40) $tasks['remark40'] = "Create REMARK 40 record for the PDB file";
//}}} Set up file/directory vars and the task list
//{{{ Run geometry programs and offer kins to user
//{{{ Ramachandran
if ($opts['chartRama']) {
$startTime = time();
setProgress($tasks, 'rama');
// updates the progress display if running as a background job
$outfile = "{$rawDir}/{$model['prefix']}rama.data";
runRamachandran($infile, $outfile);
$rama = loadRamachandran($outfile);
makeRamachandranKin($infile, "{$kinDir}/{$model['prefix']}rama.kin");
$tasks['rama'] .= " - preview <a href='viewking.php?{$_SESSION['sessTag']}&url={$kinURL}/{$model['prefix']}rama.kin' target='_blank'>kinemage</a>";
setProgress($tasks, 'rama');
// so the preview link is visible
makeRamachandranPDF($infile, "{$chartDir}/{$model['prefix']}rama.pdf");
$tasks['rama'] .= " | <a href='{$chartURL}/{$model['prefix']}rama.pdf' target='_blank'>PDF</a>\n";
setProgress($tasks, 'rama');
// so the preview link is visible
echo "Ramachandran ran for " . (time() - $startTime) . " seconds\n";
}
//}}}
//{{{ Rotamers
if ($opts['chartRota']) {
$startTime = time();
setProgress($tasks, 'rota');
// updates the progress display if running as a background job
$outfile = "{$rawDir}/{$model['prefix']}rota.data";
runRotamer($infile, $outfile);
$rota = loadRotamer($outfile);
echo "Rotamers ran for " . (time() - $startTime) . " seconds\n";
}
//}}}
//{{{ C-beta deviations
if ($opts['chartCBdev']) {
$startTime = time();
setProgress($tasks, 'cbeta');
// updates the progress display if running as a background job
$outfile = "{$rawDir}/{$model['prefix']}cbdev.data";
runCbetaDev($infile, $outfile);
$cbdev = loadCbetaDev($outfile);
makeCbetaDevPlot($infile, "{$kinDir}/{$model['prefix']}cbetadev.kin");
$tasks['cbeta'] .= " - <a href='viewking.php?{$_SESSION['sessTag']}&url={$kinURL}/{$model['prefix']}cbetadev.kin' target='_blank'>preview</a>";
setProgress($tasks, 'cbeta');
// so the preview link is visible
echo "C-beta ran for " . (time() - $startTime) . " seconds\n";
}
//}}}
//{{{ Omega peptides
if ($opts['chartOmega']) {
$startTime = time();
setProgress($tasks, 'omega');
$outfile = "{$rawDir}/{$model['prefix']}omega.data";
//$outfile = "$rawDir/$model[prefix]omega-clashlist.txt";
runOmegalyze($infile, $outfile);
$omega = loadOmegalyze($outfile);
echo "Omegalyze ran for " . (time() - $startTime) . " seconds\n";
}
//}}}
//{{{ CaBLAM
if ($opts['chartCablamLow']) {
setProgress($tasks, 'cablam');
$outfile = "{$rawDir}/{$model['prefix']}cablam.data";
runCablam($infile, $outfile);
$cablam = loadCablam($outfile);
}
//}}}
//{{{ Run nucleic acid geometry programs and offer kins to user
//{{{ Base-phosphate perpendiculars
if ($opts['chartBaseP']) {
setProgress($tasks, 'base-phos');
// updates the progress display if running as a background job
$outfile = "{$rawDir}/{$model['prefix']}pperp.data";
runBasePhosPerp($infile, $outfile);
$pperp = loadBasePhosPerp($outfile);
}
//}}}
//{{{ Suitename
if ($opts['chartSuite']) {
setProgress($tasks, 'suitename');
// updates the progress display if running as a background job
$outfile = "{$chartDir}/{$model['prefix']}suitename.txt";
runSuitenameReport($infile, $outfile);
$suites = loadSuitenameReport($outfile);
$tasks['suitename'] .= " - <a href='viewtext.php?{$_SESSION['sessTag']}&file={$outfile}&mode=plain' target='_blank'>preview</a>\n";
setProgress($tasks, 'suitename');
// so the preview link is visible
$outfile = "{$chartDir}/{$model['prefix']}suitestring.txt";
runSuitenameString($infile, $outfile);
makeSuitenameKin($infile, "{$kinDir}/{$model['prefix']}suitename.kin");
}
//}}}
//}}} Run nucleic acid geometry programs and offer kins to user
//{{{ Bonds and Angles
if ($opts['chartGeom']) {
setProgress($tasks, 'geomValidation');
// updates the progress display if running as a background job
$geomfile = "{$rawDir}/{$model['prefix']}geomvalidation.data";
runValidationReport($infile, $geomfile, $model['stats']['use_cdl']);
//$protfile = "$rawDir/$model[prefix]protvalidation.data";
//runValidationReport($infile, $protfile, "protein");
//$rnafile = "$rawDir/$model[prefix]rnavalidation.data";
//runValidationReport($infile, $rnafile, "rna");
//$validate_bond = loadValidationBondReport($protfile,"protein");
//if (is_array($validate_bond))
$validate_bond = array_merge(loadValidationBondReport($geomfile, "protein"), loadValidationBondReport($geomfile, "rna"));
if (count($validate_bond) == 0) {
$validate_bond = null;
}
$validate_angle = array_merge(loadValidationAngleReport($geomfile, "protein"), loadValidationAngleReport($geomfile, "rna"));
if (count($validate_angle) == 0) {
$validate_angle = null;
}
}
//}}}
//}}} Run programs and offer kins to user
//{{{ Run all-atom contact programs and offer kins to user
// Clashes
if ($opts['chartClashlist']) {
$startTime = time();
setProgress($tasks, 'clashlist');
// updates the progress display if running as a background job
$outfile = "{$chartDir}/{$model['prefix']}clashlist.txt";
#runClashlist($infile, $outfile, $reduce_blength);
runClashscore($infile, $outfile, $reduce_blength);
#$clash = loadClashlist($outfile);
$clash = loadClashscore($outfile);
//$clashPct = runClashStats($model['stats']['resolution'], $clash['scoreAll'], $clash['scoreBlt40']);
$tasks['clashlist'] .= " - <a href='viewtext.php?{$_SESSION['sessTag']}&file={$outfile}&mode=plain' target='_blank'>preview</a>\n";
setProgress($tasks, 'clashlist');
// so the preview link is visible
echo "chartClashlist ran for " . (time() - $startTime) . " seconds\n";
}
//}}} Run all-atom contact programs and offer kins to user
//{{{ Run real-space correlation
$model['raw_rscc_name'] = "{$model['parent']}_raw.rscc";
$model['rscc_name'] = "{$model['parent']}.rscc";
$rscc_out = "{$xrayDir}/{$model['parent']}.rscc";
$rscc_prequel_out = "{$xrayDir}/{$model['parent']}_prequel.rscc";
if ($opts['chartHoriz']) {
$startTime = time();
setProgress($tasks, 'runRSCC');
runRscc($infile, $mtz_file, $rscc_out, $rscc_prequel_out);
echo "runRscc ran for " . (time() - $startTime) . " seconds\n";
echo $mtz_file;
echo isset($mtz_file);
}
//}}}
//{{{ Report on improvements (that could be) made by MolProbity
$improveText = "";
if ($opts['chartImprove'] && ($clash || $rota)) {
$startTime = time();
setProgress($tasks, 'improve');
// updates the progress display if running as a background job
$altpdb = mpTempfile("tmp_altH_pdb_");
$mainClashscore = $clash ? $clash['scoreAll'] : 0;
$mainRotaCount = $rota ? count(findRotaOutliers($rota)) : 0;
$improvementList = array();
if ($model['isBuilt']) {
$altInpath = $modelDir . '/' . $_SESSION['models'][$model['parent']]['pdb'];
reduceNoBuild($altInpath, $altpdb, $reduce_blength);
// Rotamers
$outfile = mpTempfile("tmp_rotamer_");
runRotamer($altpdb, $outfile);
$altrota = loadRotamer($outfile);
$altRotaCount = count(findRotaOutliers($altrota));
if ($altRotaCount > $mainRotaCount) {
if ($altRotaCount - $mainRotaCount > 1) {
$improvementList[] = "fixed " . ($altRotaCount - $mainRotaCount) . " bad rotamers";
} else {
$improvementList[] = "fixed " . ($altRotaCount - $mainRotaCount) . " bad rotamer";
}
}
unlink($outfile);
// Clashes
$outfile = mpTempfile("tmp_clashlist_");
#runClashlist($altpdb, $outfile, $reduce_blength);
runClashscore($altpdb, $outfile, $reduce_blength);
#$altclash = loadClashlist($outfile);
$altclash = loadClashscore($outfile);
if ($altclash['scoreAll'] - $mainClashscore >= 0.005) {
//0.005 is the smallest change that will still be reported by the sprintf("%.2f") below
$improvementList[] = "improved your clashscore by " . sprintf("%.2f", $altclash['scoreAll'] - $mainClashscore) . " points";
}
unlink($outfile);
if (count($improvementList) > 0) {
$improveText .= "<div class='feature'>By adding H to this model and allowing Asn/Gln/His flips, you have already ";
$improveText .= implode(" and ", $improvementList);
$improveText .= ". <br /><b>Make sure you download the modified PDB to take advantage of these improvements! <br />NOTE: Atom positions have changed, so refinement to idealize geometry is necessary.</b></div>\n";
}
} elseif ($mainClashscore > 0 || $mainRotaCount > 0) {
if ($model['parent']) {
$altInpath = $_SESSION['models'][$model['parent']]['pdb'];
} else {
$altInpath = $model['pdb'];
}
$altInpath = "{$modelDir}/{$altInpath}";
reduceBuild($altInpath, $altpdb, $reduce_blength);
if ($mainRotaCount > 0) {
$outfile = mpTempfile("tmp_rotamer_");
runRotamer($altpdb, $outfile);
$altrota = loadRotamer($outfile);
$altRotaCount = count(findRotaOutliers($altrota));
if ($altRotaCount < $mainRotaCount) {
$improvementList[] = "fix " . ($mainRotaCount - $altRotaCount) . " bad rotamers";
}
unlink($outfile);
}
if ($mainClashscore > 0) {
$outfile = mpTempfile("tmp_clashlist_");
#runClashlist($altpdb, $outfile, $reduce_blength);
runClashscore($altpdb, $outfile, $reduce_blength);
#$altclash = loadClashlist($outfile);
$altclash = loadClashscore($outfile);
if ($mainClashscore - $altclash['scoreAll'] >= 0.005) {
//0.005 is the smallest change that will still be reported by the sprintf("%.2f") below
$improvementList[] = "improve your clashscore by " . sprintf("%.2f", $mainClashscore - $altclash['scoreAll']) . " points";
}
unlink($outfile);
}
if (count($improvementList) > 0) {
$improveText .= "<div class='feature'>By adding H to this model and allowing Asn/Gln/His flips, we could <i>automatically</i> ";
$improveText .= implode(" and ", $improvementList);
$improveText .= ".</div>\n";
}
}
unlink($altpdb);
echo "chart Improve ran for " . (time() - $startTime) . " seconds\n";
}
//}}} Report on improvements (that could be) made by by MolProbity
//{{{ Build multi-criterion chart, kinemage, horizontal, chart
if ($opts['doCharts']) {
$startTime = time();
if ($opts['chartMulti']) {
setProgress($tasks, 'multichart');
// updates the progress display if running as a background job
} else {
setProgress($tasks, 'chartsummary');
}
$outfile = "{$rawDir}/{$model['prefix']}multi.table";
$snapfile = "{$chartDir}/{$model['prefix']}multi.html";
$resout = "{$rawDir}/{$model['prefix']}multi_res.table";
writeMulticritChart($infile, $outfile, $snapfile, $resout, $clash, $rama, $rota, $cbdev, $pperp, $suites, $validate_bond, $validate_angle, $cablam, $omega, !$opts['chartNotJustOut'], $opts['chartMulti'], $opts['chartAltloc']);
if ($opts['chartMulti']) {
$tasks['multichart'] .= " - <a href='viewtable.php?{$_SESSION['sessTag']}&file={$outfile}' target='_blank'>preview</a>\n";
setProgress($tasks, 'multichart');
// so the preview link is visible
} else {
$tasks['chartsummary'] .= " - <a href='viewtable.php?{$_SESSION['sessTag']}&file={$outfile}' target='_blank'>preview</a>\n";
setProgress($tasks, 'chartsummary');
// so the preview link is visible
}
if ($opts['chartHoriz']) {
setProgress($tasks, 'charthoriz');
$horiz_table_file = "{$rawDir}/{$model['prefix']}horiz.table";
writeHorizontalChart($resout, $rscc_out, $outfile, $horiz_table_file, $rscc_prequel_out);
}
if ($opts['chartCoot']) {
setProgress($tasks, 'cootchart');
$outfile = "{$chartDir}/{$model['prefix']}multi-coot.scm";
$outfile_py = "{$chartDir}/{$model['prefix']}multi-coot.py";
#makeCootMulticritChart($infile, $outfile, $clash, $rama, $rota, $cbdev, $pperp);
makeCootClusteredChart($infile, $outfile, $outfile_py, $clash, $rama, $rota, $cbdev, $pperp);
}
echo "do Charts ran for " . (time() - $startTime) . " seconds\n";
}
if ($opts['doKinemage']) {
$startTime = time();
setProgress($tasks, 'multikin');
// updates the progress display if running as a background job
$mcKinOpts = array('ribbons' => $opts['kinRibbons'], 'Bscale' => $opts['kinBfactor'], 'Qscale' => $opts['kinOccupancy'], 'altconf' => $opts['kinAltConfs'], 'rama' => $opts['kinRama'], 'rota' => $opts['kinRota'], 'geom' => $opts['kinGeom'], 'cbdev' => $opts['kinCBdev'], 'omega' => $opts['kinOmega'], 'cablam' => $opts['kinCablamLow'], 'pperp' => $opts['kinBaseP'], 'clashdots' => $opts['kinClashes'], 'hbdots' => $opts['kinHbonds'], 'vdwdots' => $opts['kinContacts']);
$outfile = "{$kinDir}/{$model['prefix']}multi.kin";
$viewRes = array();
//echo "kinForceViews = ".$opts['kinForceViews']."\n";
if ($opts['kinForceViews']) {
//echo "Ran calcLocalBadness\n";
$viewRes = array_keys(calcLocalBadness($infile, 10, $clash, $rama, $rota, $cbdev, $pperp));
}
makeMulticritKin2(array($infile), $outfile, $mcKinOpts, $viewRes);
// EXPERIMENTAL: gzip compress large multikins
if (filesize($outfile) > MP_KIN_GZIP_THRESHOLD) {
destructiveGZipFile($outfile);
}
echo "do Kinemage ran for " . (time() - $startTime) . " seconds\n";
}
//}}} Build multi-criterion chart, kinemage
//{{{ Low-resolution-specific analyses
//Low-res kinemage is being simplified and merged into main kinemage
//if($opts['doLowRes'])
//{
// if($opts['kinCablamLow'] || $opts['other'])
// {
// $startTime = time();
// setProgress($tasks, 'lowResKin');
// $lowResKinOpts = array(//first column is opts, second column sets true-false
// 'ribbons' => $opts['kinRibbons'],//pass pdb w/HELIX+SHEET for this
// 'rama' => $opts['kinRama'],
// 'geom' => $opts['kinGeom'],
// 'cbdev' => $opts['kinCBdev'],
// 'omega' => $opts['kinOmega'],
// 'cablam' => $opts['kinCablamLow'],
// 'clashdots' => $opts['kinClashes']
// );
// $outfile = "$kinDir/$model[prefix]low_multi.kin";
// $cablamSecStrucFile = "$modelDir/$model[prefix]cablam_sec_struc_records.pdb";
// //$viewRes = array(); //Used with opts[kinForceViews], not necessary argument for makeMulticritKin2
// makeMulticritKinLowRes(array($infile), $outfile, $cablamSecStrucFile, $lowResKinOpts);
// if(filesize($outfile) > MP_KIN_GZIP_THRESHOLD) destructiveGZipFile($outfile);
// echo "do low-res Kinemage ran for ".(time() - $startTime)." seconds\n";
// }
//}
//}}}
//{{{ Create REMARK 40 and insert into PDB file
//if(is_array($clash) || is_array($rama) || is_array($rota))
//{
// setProgress($tasks, 'remark40'); // updates the progress display if running as a background job
// $remark40 = makeRemark40($clash, $rama, $rota);
// replacePdbRemark($infile, $remark40, 40);
//}
//}}} Create REMARK 40 and insert into PDB file
//{{{ Create lab notebook entry
$entry = "";
if (is_array($clash) || is_array($rama) || is_array($rota) || is_array($cbdev) || is_array($pperp) || is_array($suites)) {
$entry .= "<h3>Summary statistics</h3>\n";
$entry .= makeSummaryStatsTable($model['stats']['resolution'], $clash, $rama, $rota, $cbdev, $pperp, $suites, $validate_bond, $validate_angle, $cablam, $omega);
}
$entry .= $improveText;
if ($opts['doKinemage'] || $opts['doCharts']) {
$entry .= "<h3>Multi-criterion visualizations</h3>\n";
$entry .= "<div class='indent'>\n";
$entry .= "<table width='100%' border='0'><tr valign='top'>\n";
if ($opts['doKinemage']) {
$entry .= "<td>" . linkAnyFile("{$model['prefix']}multi.kin", "Kinemage", "img/multikin.jpg") . "</td>\n";
}
if ($opts['doCharts']) {
$entry .= "<td>" . linkAnyFile("{$model['prefix']}multi.table", "Chart", "img/multichart.jpg") . "</td>\n";
if ($opts['chartCoot']) {
$entry .= "<td>" . linkAnyFile("{$model['prefix']}multi-coot.scm", "To-do list for Coot", "img/multichart-coot.jpg") . "<br><small><i>Open this in Coot 0.1.2 or later using Calculate | Run Script...</i></small></td>\n";
#$entry .= "<td>".linkAnyFile("$model[prefix]multi-coot.py", "To-do list for Coot Python", "img/multichart-coot.jpg")."<br><small><i>Open this in Coot 0.1.2 or later using Calculate | Run Script...</i></small></td>\n";
}
if ($opts['chartHoriz']) {
$entry .= "<td>" . linkAnyFile("{$model['prefix']}horiz.table", "Horizontal Chart", "img/multichart_horiz.jpg") . "</td>\n";
}
}
//if($opts['doLowRes']) {
// if($opts['kinCablamLow'] || $opts['other']) {
// $entry .= "<td>".linkAnyFile("$model[prefix]low_multi.kin", "LowRes MultiKin", "img/low_multikin.jpg")."</td>\n";
// }
//}
$entry .= "</tr></table>\n";
$entry .= "</div>\n";
}
if ($opts['chartClashlist'] || $opts['chartRama'] || $opts['chartCBdev'] || $opts['chartSuite']) {
$entry .= "<h3>Single-criterion visualizations</h3>";
$entry .= "<ul>\n";
if ($opts['chartClashlist']) {
$entry .= "<li>" . linkAnyFile("{$model['prefix']}clashlist.txt", "Clash list") . "</li>\n";
}
if ($opts['chartRama']) {
$entry .= "<li>" . linkAnyFile("{$model['prefix']}rama.kin", "Ramachandran plot kinemage") . "</li>\n";
$entry .= "<li>" . linkAnyFile("{$model['prefix']}rama.pdf", "Ramachandran plot PDF") . "</li>\n";
}
if ($opts['chartCBdev']) {
$entry .= "<li>" . linkAnyFile("{$model['prefix']}cbetadev.kin", "Cβ deviation scatter plot") . "</li>\n";
}
if ($opts['chartSuite']) {
$entry .= "<li>" . linkAnyFile("{$model['prefix']}suitename.txt", "RNA backbone report") . "</li>\n";
$entry .= "<li>" . linkAnyFile("{$model['prefix']}suitestring.txt", "RNA backbone conformation \"sequence\"") . "</li>\n";
$entry .= "<li>" . linkAnyFile("{$model['prefix']}suitename.kin", "RNA backbone multi-D plot of conformations") . "</li>\n";
}
$entry .= "</ul>\n";
}
if ($remark40) {
$entry .= "<h3>REMARK 40</h3>";
$url = "{$modelURL}/{$model['pdb']}";
$entry .= "You can <a href='{$url}'>download your PDB file with REMARK 40</a> inserted, or the same <a href='download_trimmed.php?{$_SESSION['sessTag']}&file={$infile}'> without hydrogens</a>.\n";
$entry .= "<p><pre>{$remark40}</pre></p>";
}
//}}} Create lab notebook entry
setProgress($tasks, null);
// everything is finished
return $entry;
}
if (!defined('__DIR__')) {
define('__DIR__', dirname(__FILE__));
}
ini_set('max_execution_time', 60);
// The bigger this number, the longer the request will take
$max = 100000000;
/**
* Store the current progress in a file to be read by status.php
* @param $progress
*/
function setProgress($progress)
{
$file = __DIR__ . '/p';
if (!is_file($file)) {
touch($file);
}
file_put_contents($file, $progress);
}
// Loop to delay the request a lot
for ($i = 0; $i < $max; $i++) {
/**
* Each 100'000 runs, the progress will be "recorded"
* This is where you should learn what number is good for your loop that won't affect
* the requests' performance.
*/
if ($i % 100000 === 0) {
setProgress($i * 100 / $max);
}
}
echo rand(1, 100);
function setProgressOf($i, $total)
{
setProgress(percentOf($i, $total));
}
for ($i = 0; $i <= 99; $i++) {
$num = str_pad($i, 2, "0", STR_PAD_LEFT);
exec("cd {$path_something} && " . $downloader . "http://symbol.yr.no/grafikk/sym/b100/mf/01n.{$num}.png > /dev/null 2>&1 &");
usleep($sleep_time);
setProgress(++$counter, "moon");
exec("cd {$path_something} && " . $downloader . "http://symbol.yr.no/grafikk/sym/b100/mf/02n.{$num}.png > /dev/null 2>&1 &");
usleep($sleep_time);
setProgress(++$counter, "moon");
exec("cd {$path_something} && " . $downloader . "http://symbol.yr.no/grafikk/sym/b100/mf/03n.{$num}.png > /dev/null 2>&1 &");
usleep($sleep_time);
setProgress(++$counter, "moon");
exec("cd {$path_something} && " . $downloader . "http://symbol.yr.no/grafikk/sym/b100/mf/05n.{$num}.png > /dev/null 2>&1 &");
usleep($sleep_time);
setProgress(++$counter, "moon");
exec("cd {$path_something} && " . $downloader . "http://symbol.yr.no/grafikk/sym/b100/mf/06n.{$num}.png > /dev/null 2>&1 &");
usleep($sleep_time);
setProgress(++$counter, "moon");
exec("cd {$path_something} && " . $downloader . "http://symbol.yr.no/grafikk/sym/b100/mf/07n.{$num}.png > /dev/null 2>&1 &");
usleep($sleep_time);
setProgress(++$counter, "moon");
exec("cd {$path_something} && " . $downloader . "http://symbol.yr.no/grafikk/sym/b100/mf/08n.{$num}.png > /dev/null 2>&1 &");
usleep($sleep_time);
setProgress(++$counter, "moon");
}
echo "\nDone! Downloaded {$counter} files\n";
// A function to update counter
function setProgress($current, $thing)
{
global $max;
echo "\r" . chr(27) . "[K" . "Downloading... ({$thing}) ({$current} files) " . (int) ($current / $max * 100) . "%";
}
* @apiPermission Anonymous User
*
* @apiParamExample {json} Request-Example:
* {
* "unit": "42"
* }
*
* @apiSuccessExample {json} Success-Response:
* HTTP/1.1 200 OK
*
* @apiErrorExample {json} Error-Response:
* HTTP/1.1 401 Unauthorized
* {
* "error": "You are not logged in!"
* }
*
*/
$app->post('/progress/unit', function () {
$progress = json_decode(file_get_contents("php://input"), true);
setProgressViewed($progress['unit']);
});
$app->post('/progress/layer', function () {
$progress = json_decode(file_get_contents("php://input"), true);
setProgress($progress['layer'], $progress['time'], $progress['success'], $progress['score']);
});
$app->get('/progress/channel/:id', function ($id) {
getProgressChannel($id);
});
$app->get('/progress/unit/:id(/details)', function ($id) {
getProgressUnit($id, isset($_GET['details']) && $_GET['details'] == 1 ? true : false);
});
$diff .= 'pts.innerHTML = "(' . $sub . ')";';
}
if (!empty($diff)) {
?>
<script type="text/javascript">
//<![CDATA[
<?php
echo $diff;
?>
//]]>
</script>
<?php
flush();
}
}
setProgress(0, _t('최적화 작업을 진행할 테이블을 확인하고 있습니다.'));
$items = 0;
set_time_limit(0);
$item = 0;
$optimized = 0;
$tcTables = getDefinedTableNames();
$tcPluginTables = getPluginTableName();
$workarounds = array_merge($tcTables, $tcPluginTables);
$items = $items + count($tcTables) + count($tcPluginTables);
foreach ($workarounds as $work) {
setProgress($item++ / ($items * 100), _f('%1 테이블을 최적화하고 있습니다.', $work));
POD::query("OPTIMIZE TABLE {$work}");
$optimized++;
}
setProgress(100, _t('완료되었습니다.') . "({$optimized})");
finish();
function getMaps($code)
{
global $map_notebook_msg;
$map_notebook_msg = "";
$prog = getProgressTasks();
if ($_SESSION['bgjob']['eds_2fofc']) {
$prog['2fofc'] = "Download 2Fo-Fc map from the EDS";
}
if ($_SESSION['bgjob']['eds_fofc']) {
$prog['fofc'] = "Download Fo-Fc (difference) map from the EDS";
}
$mapDir = "{$_SESSION['dataDir']}/" . MP_DIR_EDMAPS;
if (!file_exists($mapDir)) {
mkdir($mapDir, 0777);
}
if ($_SESSION['bgjob']['eds_2fofc']) {
setProgress($prog, '2fofc');
$mapName = "{$code}.omap.gz";
$mapPath = "{$mapDir}/{$mapName}";
if (!file_exists($mapPame)) {
$tmpMap = getEdsMap($code, 'omap', '2fofc');
if ($tmpMap && copy($tmpMap, $mapPath)) {
unlink($tmpMap);
$_SESSION['edmaps'][$mapName] = $mapName;
mpLog("edmap-eds:User requested 2Fo-Fc map for {$code} from the EDS");
$map_notebook_msg .= "<p>The 2Fo-Fc map for {$code} was successfully retrieved from the EDS.</p>\n";
} else {
$map_notebook_msg .= "<p><div class='alert'>The 2Fo-Fc map for {$code} could not be retrieved from the EDS.</div></p>\n";
}
} else {
echo "Map file already exists";
}
}
if ($_SESSION['bgjob']['eds_fofc']) {
setProgress($prog, 'fofc');
$mapName = "{$code}-diff.omap.gz";
$mapPath = "{$mapDir}/{$mapName}";
if (!file_exists($mapPame)) {
$tmpMap = getEdsMap($code, 'omap', 'fofc');
if ($tmpMap && copy($tmpMap, $mapPath)) {
unlink($tmpMap);
$_SESSION['edmaps'][$mapName] = $mapName;
mpLog("edmap-eds:User requested Fo-Fc map for {$code} from the EDS");
$map_notebook_msg .= "<p>The Fo-Fc map for {$code} was successfully retrieved from the EDS.</p>\n";
} else {
$map_notebook_msg .= "<p><div class='alert'>The Fo-Fc map for {$code} could not be retrieved from the EDS.</div></p>\n";
}
}
}
setProgress($prog, null);
}
