function index()
{
$data = array();
$data['breadcrumb'] = set_crumbs(array(current_url() => 'Users'));
$this->load->library('pagination');
$this->load->model('users_model');
$this->load->model('groups_model');
$data['query_string'] = !empty($_SERVER['QUERY_STRING']) ? '?' . $_SERVER['QUERY_STRING'] : '';
// Hide super admin users from everyone but super admins
if ($this->Group_session->type != SUPER_ADMIN) {
$this->groups_model->where('type !=', SUPER_ADMIN);
$this->users_model->where_related_groups('type !=', SUPER_ADMIN);
}
// Get groups for group filter
$data['Groups'] = $this->groups_model->get();
// Process Filter Using Admin Helper
$filter = process_filter('users');
// Filter results by search query
if (isset($filter['search'])) {
$this->users_model->where("(concat_ws(' ', first_name, last_name) LIKE '%{$filter['search']}%' OR email LIKE '%{$filter['search']}%')");
}
// Filter results by group
if (isset($filter['group_id'])) {
$this->users_model->where("group_id", $filter['group_id']);
}
$per_page = 50;
// Query
$data['Users'] = $this->users_model->order_by($this->input->get('sort') ? $this->input->get('sort') : 'last_name', $this->input->get('order') ? $this->input->get('order') : 'asc')->include_related('groups', 'name')->get_paged($this->uri->segment(4), $per_page, TRUE);
$config['base_url'] = site_url(ADMIN_PATH . '/users/index/');
$config['per_page'] = $per_page;
$config['uri_segment'] = '4';
$config['num_links'] = 5;
$config['suffix'] = $data['query_string'];
$config['total_rows'] = $data['Users']->paged->total_rows;
$this->pagination->initialize($config);
$this->template->view('admin/users/users', $data);
}
function index()
{
$data = array();
$data['breadcrumb'] = set_crumbs(array(current_url() => 'Pages'));
// Load libraries and models
$this->load->model('entries_model');
$this->load->model('content_types_model');
$this->load->model('revisions_model');
$this->load->library('pagination');
$data['query_string'] = !empty($_SERVER['QUERY_STRING']) ? '?' . $_SERVER['QUERY_STRING'] : '';
$data['content_types_filter'] = array('' => '');
$data['content_types_add_entry'] = array();
// Process Filter using Admin Helper
$filter = process_filter('entries');
// Define fields the search filter searches
$search = array();
if (isset($filter['search'])) {
$search['title'] = $filter['search'];
$search['slug'] = $filter['search'];
$search['id'] = $filter['search'];
unset($filter['search']);
}
// Pagination Settings
$per_page = 50;
// If user not a super admin only get the content types and entires allowed for access
if ($this->Group_session->type != SUPER_ADMIN) {
$this->content_types_model->where('restrict_admin_access', 0)->or_where_related('admin_groups', 'group_id', $this->Group_session->id);
$this->entries_model->group_start()->where('restrict_admin_access', 0)->or_where_related('content_types/admin_groups', 'group_id', $this->Group_session->id)->group_end();
}
// Build content type filter dropdown
// and add entry's list of content types
$Content_types = $this->content_types_model->order_by('title', 'asc')->get();
foreach ($Content_types as $Content_type) {
$entries_count = $Content_type->entries->count();
// Only add the content type to the Add Entry dropdown if it has not reached the
// limit of entries allowed. An empty entries_allowed is unlimited
if ($Content_type->entries_allowed == '' || $entries_count < $Content_type->entries_allowed || $entries_count == 0 && $Content_type->entries_allowed > 0) {
$data['content_types_add_entry'][$Content_type->id] = $Content_type->title;
}
// Only add the content type to the filter dropdown if it has one or more entries
if ($entries_count > 0) {
$data['content_types_filter'][$Content_type->id] = $Content_type->title;
}
}
$this->entries_model->include_related('content_types', 'title');
// Filter by search string
if (!empty($search)) {
$this->entries_model->group_start()->or_like($search)->group_end();
}
// Filter by dropdowns
if (!empty($filter)) {
$this->entries_model->group_start()->where($filter)->group_end();
}
// Finalize and sort entries query
$data['Entries'] = $this->entries_model->order_by($this->input->get('sort') ? $this->input->get('sort') : 'modified_date', $this->input->get('order') ? $this->input->get('order') : 'desc')->get_paged($this->uri->segment(5), $per_page, TRUE);
// Create Pagination
$config['base_url'] = site_url(ADMIN_PATH . '/content/entries/index/');
$config['total_rows'] = $data['Entries']->paged->total_rows;
$config['per_page'] = $per_page;
$config['uri_segment'] = '5';
$config['num_links'] = 5;
$config['suffix'] = $data['query_string'];
$this->pagination->initialize($config);
$this->template->view('admin/entries/entries', $data);
}
$page = isset($_GET['p']) ? $_GET['p'] : 1; $per_page = isset($_GET['pp']) ? $_GET['pp'] : 10; // Connect to the database $db = db_connect($database); // Save these variables for automatic URL formation later on. $display = array(); $display['id'] = $batch_id; $display['db'] = $database; $display['p'] = $page; $display['pp'] = $per_page; $display['filter_type'] = array(); // // Process the filtering parameters // $param = array($batch_id); process_filter($display); prepare_filter_parameters($display, $param); // // Prepare some SQL queries // $query = "SELECT batches.id as id, date, description, type FROM batches " . "WHERE batches.id=?"; $db['batch_sth'] = $db['dbh']->prepare($query); check_db_error($db['batch_sth'], __FILE__, __LINE__); $query = "SELECT COUNT(tag_id) as count FROM catalog_index " . "WHERE batch_id=?"; $query .= apply_query_filters($display); $db['count_sth'] = $db['dbh']->prepare($query); check_db_error($db['count_sth'], __FILE__, __LINE__); $query = "SELECT alleles as count FROM catalog_index " . "WHERE batch_id=? AND tag_id=?"; $db['allele_sth'] = $db['dbh']->prepare($query); check_db_error($db['allele_sth'], __FILE__, __LINE__); $query = "SELECT col, rank_2 FROM catalog_snps " . "JOIN batches ON (catalog_snps.batch_id=batches.id) " . "WHERE batch_id=? AND tag_id=? ORDER BY col";
function process_geomap($MAPCFG, $map_name, &$map_config)
{
$params = $MAPCFG->getSourceParams();
list($image_name, $image_path, $data_path) = geomap_files($params);
// Load the list of locations
$locations = geomap_get_locations($params);
// This source does not directly honor the existing map configs. It saves
// the existing config to use it later for modifying some object parameters.
// The existing map config must not create new objects. The truth about the
// existing objects comes only from this source.
$saved_config = $map_config;
$map_config = array();
$iconset = $params['iconset'];
list($icon_w, $icon_h) = iconset_size($iconset);
// Adapt the global section
$map_config[0] = $saved_config[0];
$map_config[0]['map_image'] = $image_name . '?' . time() . '.png';
$map_config[0]['iconset'] = $iconset;
// Now add the objects to the map
foreach ($locations as $loc) {
$object_id = $MAPCFG->genObjId($loc['name']);
$map_config[$object_id] = array('type' => 'host', 'host_name' => $loc['name'], 'iconset' => $iconset, 'object_id' => $object_id, 'alias' => $loc['alias'], 'lat' => $loc['lat'], 'long' => $loc['long']);
if (isset($loc['backend_id'])) {
$map_config[$object_id]['backend_id'] = array($loc['backend_id']);
}
}
unset($locations);
// Now apply the filters. Though the map can be scaled by the filtered hosts
process_filter($MAPCFG, $map_name, $map_config, $params);
// Terminate empty views
if (count($map_config) <= 1) {
throw new GeomapError(l('Got empty map after filtering. Terminate rendering geomap.'));
}
// Now detect the upper and lower bounds of the locations to display
// Left/upper and right/bottom
// north/south
$min_lat = 90;
$max_lat = -90;
// east/west
$min_long = 180;
$max_long = -180;
foreach ($map_config as $obj) {
if ($obj['type'] == 'global') {
continue;
}
if ($obj['lat'] < $min_lat) {
$min_lat = $obj['lat'];
}
if ($obj['lat'] > $max_lat) {
$max_lat = $obj['lat'];
}
if ($obj['long'] < $min_long) {
$min_long = $obj['long'];
}
if ($obj['long'] > $max_long) {
$max_long = $obj['long'];
}
}
// Fix equal coordinates (Simply add some space on all sides)
$min_lat -= $params['geomap_border'];
$max_lat += $params['geomap_border'];
$min_long -= $params['geomap_border'];
$max_long += $params['geomap_border'];
// FIXME: Too small min/max? What is the minimum bbox size?
//echo $min_lat . ' - ' . $max_lat. ' - '. $mid_lat.'\n';
//echo $min_long . ' - ' . $max_long. ' - ' . $mid_long;
if (!$params['width'] || !$params['height']) {
throw new GeomapError(l('Missing mandatory "width" and "height" parameters."'));
}
// Using this API: http://pafciu17.dev.openstreetmap.org/
$url = cfg('global', 'geomap_server') . '?module=map' . '&width=' . $params['width'] . '&height=' . $params['height'] . '&type=' . $params['geomap_type'];
// The geomap zoom seems to be something different than the nagvis zoom. Use
// the dedicated geomap_zoom parameter
if (isset($params['geomap_zoom']) && $params['geomap_zoom'] != '') {
$mid_lat = ($min_lat + $max_lat) / 2;
$mid_long = ($min_long + $max_long) / 2;
$url .= '&zoom=' . $params['geomap_zoom'] . '¢er=' . $mid_long . ',' . $mid_lat;
} else {
$url .= '&bbox=' . $min_long . ',' . $max_lat . ',' . $max_long . ',' . $min_lat;
}
//file_put_contents('/tmp/123', $url);
// Fetch the background image when needed
if (!file_exists($image_path) || geomap_source_age($params) > filemtime($image_path)) {
// Allow/enable proxy
$contents = geomap_get_contents($url);
file_put_contents($image_path, $contents);
}
// Fetch the map bounds when needed
if (!file_exists($data_path) || geomap_source_age($params) > filemtime($data_path)) {
// Get the lat/long of the image bounds. The api adds a border area to the
// generated image. This is good since this makes the outer nodes not touch
// the border of the image. But this makes calculation of the x/y coords
// problematic. I found a parameter which tells us the long/lat coordinates
// of the image bounds.
// http://pafciu17.dev.openstreetmap.org/?module=map&bbox=6.66748,53.7278,14.5533,51.05&width=1500&height=557&type=osmarender&bboxReturnFormat=csv
// 2.373046875,54.239550531562,18.8525390625,50.499452103968
$data_url = $url . '&bboxReturnFormat=csv';
$contents = geomap_get_contents($data_url);
if (!$contents || ord($contents[0]) == 137 && ord($contents[1]) == 80 && ord($contents[2]) == 78) {
// Got an png image as answer - catch this!
throw new GeomapError(l('Got invalid response from "[U]". This is mostly caused by an unhandled request.', array('U' => $data_url)));
}
if (!preg_match('/^-?[0-9]+\\.?[0-9]*,-?[0-9]+\\.?[0-9]*,-?[0-9]+\\.?[0-9]*,-?[0-9]+\\.?[0-9]*$/i', $contents)) {
throw new GeomapError(l('Got invalid data from "[U]": "[C]"', array('U' => $data_url, 'C' => json_encode($contents))));
}
file_put_contents($data_path, $contents);
$parts = explode(',', $contents);
} else {
$parts = explode(',', file_get_contents($data_path));
}
$img_left = (double) $parts[0];
$img_top = (double) $parts[1];
$img_right = (double) $parts[2];
$img_down = (double) $parts[3];
$long_diff = $img_right - $img_left;
$lat_diff = $img_top - $img_down;
$long_para = $params['width'] / $long_diff;
$lat_para = $params['height'] / $lat_diff;
$lat_mult = $params['height'] / (ProjectF($img_top) - ProjectF($img_down));
// Now add the coordinates to the map objects
foreach ($map_config as &$obj) {
if (!isset($obj['lat'])) {
continue;
}
// Calculate the lat (y) coords
$obj['y'] = round((ProjectF($img_top) - ProjectF($obj['lat'])) * $lat_mult - $icon_h / 2);
if ($obj['y'] < 0) {
$obj['y'] = 0;
}
// Calculate the long (x) coords
$obj['x'] = round($long_para * ($obj['long'] - $img_left) - $icon_w / 2);
if ($obj['x'] < 0) {
$obj['x'] = 0;
}
unset($obj['lat']);
unset($obj['long']);
}
return true;
// allow caching
}
/**
* A source can modify the map configuration before it is used for further processing.
* Such a source is a key which points to a "process", "params" and "changed" function
* which can
* 1. modify the map config array
* 2. gather all the parameters used in this source
* 3. tell the source processing that the data used in this source has changed and the
* source needs processed again
*/
private function processSources()
{
global $_MAINCFG;
$sources = $this->getValue(0, 'sources');
if (!$sources) {
return;
}
// 1. Check if there is a cache file for a query with this params
$params = $this->getSourceParams();
// FIXME: Add a flag to exclude options from cache file naming
if (isset($params['source_file'])) {
unset($params['source_file']);
}
$param_values = $this->paramsToString($params);
$cacheFile = cfg('paths', 'var') . 'source-' . $this->name . '.cfg-' . $param_values . '-' . CONST_VERSION . '.cache';
$CACHE = new GlobalFileCache(array(), $cacheFile);
// 2a. Check if the cache file exists
// 2b. Check if the cache file is newer than the latest changed source
$cache_sources = $CACHE->isCached();
$cache_map = $this->CACHE->isCached();
$cache_maincfg = $_MAINCFG->isCached();
if ($cache_sources != -1 && $cache_map != -1 && $cache_maincfg != -1 && $cache_sources >= $cache_maincfg && $cache_sources >= $cache_map && !$this->sourcesChanged($cache_sources)) {
// 3a. Use the cache
$this->mapConfig = $CACHE->getCache();
return;
}
$cacheable = true;
// 3b. Process all the sources
foreach ($sources as $source) {
$func = 'process_' . $source;
if (!function_exists($func)) {
throw new NagVisException(l('Requested source "[S]" does not exist', array('S' => $source)));
}
try {
$cacheable &= $func($this, $this->name, $this->mapConfig);
} catch (Exception $e) {
if (!$this->ignoreSourceErrors) {
throw $e;
}
}
}
// Call process filter implicit if not already done
process_filter($this, $this->name, $this->mapConfig);
if ($cacheable) {
$CACHE->writeCache($this->mapConfig, 1);
}
// FIXME: Invalidate/remove cache files on changed configurations
}
$q[] = "by={$by}";
$title .= (!isset($type) ? 'Entries ' : '') . "by {$by} ";
}
} else {
if (isset($q)) {
$q[] = 'by=' . CoreUtils::FIXPATH_EMPTY;
}
}
}
$q = array();
if (isset($_GET['js'])) {
$q[] = 'js=' . $_GET['js'];
}
process_filter($q);
$Pagination = new Pagination('admin/logs', 20, $Database->count('log'));
$heading = 'Global logs';
if (!empty($title)) {
$title .= '- ';
}
$title .= "Page {$Pagination->page} - {$heading}";
CoreUtils::fixPath("/admin/logs/{$Pagination->page}" . (!empty($q) ? '?' . implode('&', $q) : ''));
process_filter();
$LogItems = $Database->orderBy('timestamp')->orderBy('entryid')->get('log', $Pagination->getLimit());
if (isset($_GET['js'])) {
$Pagination->respond(Logs::getTbody($LogItems), '#logs tbody');
}
CoreUtils::loadPage(array('title' => $title, 'view' => "{$do}-logs", 'css' => "{$do}-logs", 'js' => array("{$do}-logs", 'paginate')));
break;
default:
CoreUtils::notFound();
}
$batch_id = isset($_GET['id']) ? $_GET['id'] : 0;
$email = isset($_GET['email']) ? $_GET['email'] : "";
$data_type = isset($_GET['dtype']) ? $_GET['dtype'] : "haplo";
$map_type = isset($_GET['mtype']) ? $_GET['mtype'] : "gen";
$depth_lim = isset($_GET['dlim']) ? $_GET['dlim'] : "1";
$man_cor = isset($_GET['mcor']) ? $_GET['mcor'] : "0";
$ex_type = isset($_GET['otype']) ? $_GET['otype'] : "tsv";
// Connect to the database
$db = db_connect($database);
// Save these variables for automatic URL formation later on.
$display = array();
$display['id'] = $batch_id;
$display['db'] = $database;
$display['filter_type'] = array();
$filters = array();
process_filter($display, $filters);
//
// Create a new catalog object to hold filtered loci
//
$catalog = new Catalog($db, $batch_id, $display);
$catalog->determine_count();
$loci_cnt = $catalog->num_loci();
$mc = $man_cor > 0 ? "-c" : "";
if ($data_type == "haplo") {
$dt = "-a haplo";
$dl = "-L {$depth_lim}";
} else {
if ($data_type == "geno") {
$dt = "-a geno -m {$map_type} {$mc}";
$dl = "";
}
