function tearDown()
{
// Remove created beans.
foreach ($this->to_remove as $object) {
if (is_a($object, 'SugarBean')) {
$table = $object->getTableName();
$object->mark_deleted($object->id);
$this->db->query("DELETE FROM {$table} WHERE id = '{$object->id}' ");
$this->db->query("DELETE FROM {$table}_audit WHERE parent_id = '{$object->id}' ");
unset($object);
}
}
$this->to_remove = array();
}
/**
*
* Enter description here ...
* @param unknown_type $db
* @param array $bp start ende chr ens_species
*/
function getSyntenyRegionIDs($db, $bp)
{
$species = strtolower($bp[3]);
if ($species == 'mus_musculus') {
$genome_db_id = 57;
} elseif ($species == 'rattus_norvegicus') {
$genome_db_id = 3;
} elseif ($species == 'homo_sapiens') {
$genome_db_id = 90;
}
$sqlDnafrag = 'SELECT dfr.synteny_region_id FROM dnafrag_region as dfr INNER JOIN
dnafrag as df ON (dfr.dnafrag_start <= ' . $bp[1] . ' AND
dfr.dnafrag_end >= ' . $bp[0] . ' AND
dfr.dnafrag_id = df.dnafrag_id AND
df.name = "' . $bp[2] . '" AND
df.genome_db_id = ' . $genome_db_id . ');';
$fragQuery = $db->query($sqlDnafrag) or fatal_error('Query failed: ' . $db->error);
//$frag_table = $fragQuery->fetch_all();
$str = "";
$first = true;
while ($row = $fragQuery->fetch_assoc()) {
if ($first) {
$str .= $row['synteny_region_id'];
$first = false;
} else {
$str .= "," . $row['synteny_region_id'];
}
}
$fragQuery->close();
return $str;
}
/**
* (non-PHPdoc)
* @see IBrowserService::searchAll()
*/
public function searchAll($search, $columns, $offset, $num, $sort, $sortDirection = 'asc', $isCount = false)
{
$whereSqlParts = array();
foreach ($columns as $column) {
// get db column name
$columnName = $this->propertyToColumnMapping[$column];
$whereSqlParts[] = "{$column} LIKE '%{$search}%'";
}
// build where clause for all columns we are searching against
$whereSql = implode($whereSqlParts, ' OR ');
// check if we just need a count of results
if ($isCount) {
$query = "SELECT count(*) as count FROM browsers WHERE {$whereSql}";
$statement = $this->connection->query($query);
$result = $statement->fetch();
return $result['count'];
} else {
$sort = $this->propertyToColumnMapping[$sort];
$query = "SELECT *\n \t\t\t\tFROM\n \t\t\t\t browsers\n \t\t\t \tWHERE\n \t\t\t {$whereSql}\n \t\t\t \tORDER BY \n \t\t\t {$sort} {$sortDirection}\n \t\t\t \tLIMIT\n \t\t\t {$offset}, {$num}";
$statement = $this->connection->query($query);
$results = $statement->fetchAll();
$browsers = $this->hydrateResults($results);
return $browsers;
}
}
/**
* Actualiza el perfil del usuario registrado en el sitio. Los datos
* del perfil actualizados son: correo e idioma.
*/
public function updateProfile()
{
try {
// se obtiene el correo del usuario
$email = JUser::getInstance(JFactory::getUser()->id)->email;
// se establece el valor del idioma
$language = JFactory::getUser()->getParam('language');
if (strcmp($language, 'ca-ES') == 0) {
$language = 'catalan';
} else {
if (strcmp($language, 'es-ES') == 0) {
$language = 'spanish';
} else {
$language = 'english';
}
}
// se obtiene el nombre del usuario
$username = $this->currentUser;
// se actualiza el idioma
$query = str_replace('%language%', $language, getQuery('updateLanguage'));
$query = str_replace('%username%', $username, $query);
$resultQuery = $this->proxyMySql->query($query);
// se actualiza el correo
$query = str_replace('%email%', $email, getQuery('updateEmail'));
$query = str_replace('%username%', $username, $query);
$resultQuery = $this->proxyMySql->query($query);
} catch (Exception $e) {
}
}
/**
* @name function generarUbicacion
* @param unknown_type $db coneccion
* @param entero $codigo
* @param entero $bandera
* @return String
*/
function generarUbicacion($db, $codigo, $bandera)
{
$query = "select SGD_EIT_NOMBRE,SGD_EIT_CODIGO,SGD_EIT_COD_PADRE,CODI_DPTO,CODI_MUNI from SGD_EIT_ITEMS where SGD_EIT_CODIGO= '{$codigo}' order by SGD_EIT_NOMBRE";
$rs = $db->query($query);
$son = explode(" ", $rs->fields["SGD_EIT_NOMBRE"]);
if ($rs->fields["SGD_EIT_COD_PADRE"] == 0) {
$query = "select distinct(m.MUNI_NOMB),m.MUNI_CODI FROM MUNICIPIO m , SGD_EIT_ITEMS i WHERE m.MUNI_CODI=i.CODI_MUNI and DPTO_CODI='" . $rs->fields['CODI_DPTO'] . "' and MUNI_CODI='" . $rs->fields['CODI_MUNI'] . "' ORDER BY MUNI_NOMB";
$rs1 = $db->query($query);
$queryDpto = "select distinct(d.DPTO_NOMB),d.DPTO_CODI FROM DEPARTAMENTO d, SGD_EIT_ITEMS i WHERE d.DPTO_CODI=i.CODI_DPTO and i.CODI_DPTO=" . $rs->fields['CODI_DPTO'] . "ORDER BY DPTO_NOMB";
$rs2 = $db->query($queryDpto);
$depto = "<TABLE width='100%' border=0><tr><td width='25%' class='titulos2'>DEPARTAMENTO</td> <td width='25%' class='titulos2'>" . $rs2->fields["DPTO_NOMB"] . "</td>";
$muni = "<td width='25%' class='titulos2'>MUNICIPIO</td> <td width='25%' class='titulos2'>" . $rs1->fields["MUNI_NOMB"] . "</td></TR>";
$edificio = "<tr><td width='25%' class='titulos2'>EDIFICIO</td> <td width='25%' class='titulos2'> <input type=\"hidden\" name=\"exp_edificio2\" id=\"exp_edificio2\" value='" . $rs->fields["SGD_EIT_CODIGO"] . "'>" . $rs->fields["SGD_EIT_NOMBRE"] . " \n\t\t\n\t\t\n\t\t</td>";
$option[0] = $depto . $muni . $edificio;
$option[1] = 2;
return $option;
} else {
$ban = $bandera + 1;
$option = generarUbicacion($db, $rs->fields["SGD_EIT_COD_PADRE"], $ban);
//$son=explode(" ",$rs->fields["SGD_EIT_NOMBRE"]);
//substr('abcdef', 0, 4);
if (substr($son[0], 0, 4) == 'PISO' || substr($son[0], 0, 6) == 'SOTANO') {
$option[0] .= "<td width='25%' class='titulos2'>PISO</td> <td width='25%' class='titulos2'>" . $rs->fields["SGD_EIT_NOMBRE"] . "<input type=\"hidden\" name=\"exp_piso2\" id=\"exp_piso2\" value='" . $rs->fields["SGD_EIT_CODIGO"] . "' /></td></tr> \n";
$option[1] = 1;
return $option;
} else {
if ($option[1] == 1) {
$option[0] .= "<tr>";
$opt = 2;
}
$option[0] .= "<td width='25%' class='titulos2'>" . $son[0] . "</td> <td width='25%' class='titulos2'> " . $rs->fields["SGD_EIT_NOMBRE"] . "</td>";
if ($option[1] == 2) {
$option[0] .= "</tr>";
$opt = 1;
}
if ($bandera == 0) {
if ($option[1] == 1) {
$option[0] .= "</tr>";
}
return $option[0] . "</table>";
} else {
$option[1] = $opt;
return $option;
}
}
}
}
/**
* 获取$sql查询中结果的总条数
* @param unknown_type $sql
* @return number
*/
public function count_query($sql)
{
$res = $this->db->query($sql)->result();
if (empty($res)) {
return 0;
}
return count($res);
}
/**
* Create Term and Taxonomy Relationships.
*
* Relates an object (post, link etc) to a term and taxonomy type. Creates the
* term and taxonomy relationship if it doesn't already exist. Creates a term if
* it doesn't exist (using the slug).
*
* A relationship means that the term is grouped in or belongs to the taxonomy.
* A term has no meaning until it is given context by defining which taxonomy it
* exists under.
*
* @package NXTClass
* @subpackage Taxonomy
* @since 2.3.0
*
* @param int $object_id The object to relate to.
* @param array|int|string $term The slug or id of the term, will replace all existing
* related terms in this taxonomy.
* @param array|string $taxonomy The context in which to relate the term to the object.
* @param bool $append If false will delete difference of terms.
* @return array|nxt_Error Affected Term IDs
*/
function set_object_terms($object_id, $terms, $taxonomy, $append = false)
{
$object_id = (int) $object_id;
if (!$this->is_taxonomy($taxonomy)) {
return new nxt_Error('invalid_taxonomy', __('Invalid Taxonomy'));
}
if (!is_array($terms)) {
$terms = array($terms);
}
if (!$append) {
$old_tt_ids = $this->get_object_terms($object_id, $taxonomy, array('fields' => 'tt_ids', 'orderby' => 'none'));
}
$tt_ids = array();
$term_ids = array();
foreach ((array) $terms as $term) {
if (!strlen(trim($term))) {
continue;
}
if (!($id = $this->is_term($term, $taxonomy))) {
$id = $this->insert_term($term, $taxonomy);
}
if (is_nxt_error($id)) {
return $id;
}
$term_ids[] = $id['term_id'];
$id = $id['term_taxonomy_id'];
$tt_ids[] = $id;
if ($this->db->get_var($this->db->prepare("SELECT term_taxonomy_id FROM {$this->db->term_relationships} WHERE object_id = %d AND term_taxonomy_id = %d", $object_id, $id))) {
continue;
}
$this->db->insert($this->db->term_relationships, array('object_id' => $object_id, 'term_taxonomy_id' => $id));
}
$this->update_term_count($tt_ids, $taxonomy);
if (!$append) {
$delete_terms = array_diff($old_tt_ids, $tt_ids);
if ($delete_terms) {
$in_delete_terms = "'" . implode("', '", $delete_terms) . "'";
$this->db->query($this->db->prepare("DELETE FROM {$this->db->term_relationships} WHERE object_id = %d AND term_taxonomy_id IN ({$in_delete_terms})", $object_id));
$this->update_term_count($delete_terms, $taxonomy);
}
}
$t = $this->get_taxonomy($taxonomy);
if (!$append && isset($t->sort) && $t->sort) {
$values = array();
$term_order = 0;
$final_tt_ids = $this->get_object_terms($object_id, $taxonomy, 'fields=tt_ids');
foreach ($tt_ids as $tt_id) {
if (in_array($tt_id, $final_tt_ids)) {
$values[] = $this->db->prepare("(%d, %d, %d)", $object_id, $tt_id, ++$term_order);
}
}
if ($values) {
$this->db->query("INSERT INTO {$this->db->term_relationships} (object_id, term_taxonomy_id, term_order) VALUES " . join(',', $values) . " ON DUPLICATE KEY UPDATE term_order = VALUES(term_order)");
}
}
do_action('set_object_terms', $object_id, $terms, $tt_ids, $taxonomy, $append);
return $tt_ids;
}
/**
* The construct get all allowedsites in the beginn..
* @param unknown_type $connection
*/
public function __construct($connection)
{
$query = $connection->query('SELECT * FROM `config_loginneedlesssites`');
echo $query;
if ($query != "") {
foreach ($query as $siterow) {
$allowedSite = new allowedSite();
$allowedSite->setId($siterow['id']);
$allowedSite->setName($siterow['site']);
array_push($this->allAllowedSites, $allowedSite);
}
}
}
/**
* SELAA 12 UUSINTA PROJEKTIA!
* Hakee annetusta kannasta enintään 12 uusinta projektia.
* @param unknown_type $DBH
* @return $projektit taulukko
*/
function getNewProjects($DBH)
{
try {
//Haetaan 12 uusinta projektia
$projektit = array();
//Taulukko projekti-olioille
$STH = $DBH->query("SELECT projekti.nimi, projekti.kuva \n\t\t\t\t FROM projekti\n\t\t\t\t ORDER BY projekti.pvm DESC LIMIT 12");
//DESC,ASC
$STH->setFetchMode(PDO::FETCH_OBJ);
//yksi rivi objektina
return $projektit;
} catch (PDOException $e) {
//Kirjoitetaan mahdollinen virheviesti tiedostoon
file_put_contents('log/DBErrors.txt', 'selaa.php: ' . $e->getMessage() . "\n", FILE_APPEND);
return false;
}
}
/**
* Show columns of current table
*
* @return Array
*/
public function queryColumns()
{
if (empty(self::$cache[static::$table])) {
// temporaire...
if ($this->db->getDriver() == 'mysql') {
$s = $this->db->query("SHOW COLUMNS FROM " . static::$table);
} elseif ($this->db->getDriver() == 'pgsql') {
$s = $this->db->prepare("SELECT column_name AS field FROM information_schema.columns WHERE table_name=?");
$s->execute(array(static::$table));
}
if ($s->rowCount() <= 0) {
throw new LiException('La table ' . $table . ' ne contient aucune colonne');
}
$rs = $s->fetchAll();
$fields = array();
foreach ($rs as $row) {
$fields[] = $row['field'];
}
self::$cache[static::$table] = $fields;
}
return self::$cache[static::$table];
}
/**
* get the homologue ensemble ids of the target species to a given set of ensebl ids.
*
* @param unknown_type $compara
* @param unknown_type $unique_ids
* @param $target_species_name the name of the target species for filtering (speed up)
* @author g 2011.04.26
*/
function get_homologue_ens_ids($compara, $unique_ids, $target_species_name)
{
$sql = 'SELECT m.stable_id, m2.stable_id, hom.description
FROM member AS m
INNER JOIN homology_member AS h ON (
m.member_id = h.member_id
AND m.genome_db_id = (SELECT genome_db_id FROM genome_db WHERE name="' . $target_species_name . '")
) INNER join homology AS hom ON (
h.homology_id = hom.homology_id
) INNER join homology_member AS h2 on (
h.homology_id = h2.homology_id
) INNER join member AS m2 on (
m2.member_id = h2.member_id AND m2.stable_id IN ("' . implode('","', $unique_ids) . '")
) GROUP BY m.stable_id, m2.stable_id;';
$result = $compara->query($sql) or fatal_error($compara->error);
$homology = array_combine($unique_ids, array_fill(0, count($unique_ids), array()));
while ($row = $result->fetch_row()) {
$homology[$row[1]][$row[0]] = $row[2];
}
$result->close();
return $homology;
}
/**
* Resolve a username with a id..
* @param unknown_type $userid
* @param unknown_type $connection
*/
public static function getUserById($userid, $connection)
{
foreach ($connection->query('SELECT * FROM user WHERE uid="' . $userid . '";') as $userrow) {
return $userrow['username'];
}
}
/**
* Get all the roles
* @param unknown_type $connection
*/
public static function getRoles($connection)
{
$tmp = $connection->query("SELECT * FROM role;");
return $tmp->fetchAll();
}
