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complex
Commit 68574d69 authored by Niklas Mähler's avatar Niklas Mähler
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Use central config file for credentials

parent 354d4c14
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Showing with 6170 additions and 4 deletions
.gitignore
View file @ 68574d69
service
service/*
junk
junk/*
local_config.php
config.php 0 → 100644
View file @ 68574d69
<?php
$config = array();
$config["db"]["host"] = null;
$config["db"]["user"] = null;
$config["db"]["password"] = null;
$config["db"]["database"] = null;
$config["basket_db"]["host"] = null;
$config["basket_db"]["user"] = null;
$config["basket_db"]["password"] = null;
$config["basket_db"]["database"] = null;
require_once("local_config.php");
?>
db.php
View file @ 68574d69
<?php
require_once("config.php");
//$dbConn = mysql_connect($data[0],$data[1],$ps[$i])or die("Could not connect");
$dbConn = mysql_connect("localhost","popuser","poppass")or die("Could not connect");
$db = mysql_select_db("plazacomplex", $dbConn) or die("Could not select DB");
$dbConn = mysql_connect(
$config["db"]["host"],
$config["db"]["user"],
$config["db"]["password"]
)or die("Could not connect");
$db = mysql_select_db("plaza_complex", $dbConn) or die("Could not select DB");
$spNames = array("pt" => "P. Triocharpa", "at" => "A. Thaliana", "os" => "O. Sativa");
......
service/ActiveRecords/mysql.php 0 → 100755
View file @ 68574d69
<?php
/**
* Ignited Datatables ActiveRecords library for MySql
*
* @subpackage libraries
* @category library
* @version 0.1
* @author Yusuf Ozdemir <yusuf@ozdemir.be>
*/
class ActiveRecords
{
/**
* Variables
*
*/
var $ar_select = array();
var $ar_from = array();
var $ar_join = array();
var $ar_where = array();
var $ar_orderby = array();
var $ar_limit = FALSE;
var $ar_offset = FALSE;
var $ar_order = FALSE;
var $_escape_char = '`';
var $_count_string = 'SELECT COUNT(*) AS ';
var $username = 'root';
var $password = '';
var $database = '';
var $hostname = 'localhost';
var $port = '';
var $db ;
var $_result;
/**
* Construct function
*
*/
public function connect($config)
{
foreach ($config as $key => $val)
if(in_array($key, array('hostname', 'username', 'password', 'database', 'port')))
$this->$key = $val;
$this->db_connect();
$this->db_select();
}
/**
* DB connection
*
*/
protected function db_connect()
{
if ($this->port != '')
$this->hostname .= ':'.$this->port;
$this->db = @mysql_connect($this->hostname, $this->username, $this->password, TRUE);
}
/**
* DB Select
*
*/
protected function db_select()
{
@mysql_select_db( $this->database, $this->db ) or
die( 'Could not select database ' . $this->database );
}
/**
* Generates the SELECT portion of the query
*
*/
public function select($columns, $backtick_protect = TRUE)
{
foreach ($columns as $column)
$this->ar_select[] = ($backtick_protect == TRUE)? $this->_protect_identifiers(trim($column)) : trim($column);
return $this;
}
/**
* Generates the FROM portion of the query
*
*/
public function from($from)
{
foreach ((array)$from as $f)
$this->ar_from[] = $this->_protect_identifiers(trim($f));
return $this;
}
/**
* Generates the JOIN portion of the query
*
*/
public function join($table, $cond, $type = '')
{
if ($type != '')
{
$type = strtoupper(trim($type));
$type = (!in_array($type, array('LEFT', 'RIGHT', 'OUTER', 'INNER', 'LEFT OUTER', 'RIGHT OUTER')))? '':$type.' ' ;
}
$join = $type.'JOIN '.$this->_protect_identifiers($table).' ON '.$this->_protect_identifiers($cond);
$this->ar_join[] = $join;
return $this;
}
/**
* Generates the WHERE portion of the query
*
*/
public function where($key, $value = NULL, $escape = TRUE, $type = 'AND ')
{
if ( ! is_array($key))
$key = array($key => $value);
foreach ($key as $k => $v)
{
$prefix = (count($this->ar_where) == 0)? '' : $type;
if($v != NULL)
{
$k = ($this->_has_operator($k) == TRUE)? $k : $k . ' =';
$v = ($escape == TRUE)? " '" . $v . "'" : $v;
}
$this->ar_where[] = $prefix . (($escape == TRUE)? $this->_protect_identifiers($k.$v) : $k.$v);
}
return $this;
}
/**
* Generates the LIMIT portion of the query
*
*/
public function limit($value, $offset = '')
{
$this->ar_limit = $value;
if ($offset != '')
$this->ar_offset = $offset;
return $this;
}
/**
* Generates the ORDER BY portion of the query
*
*/
public function order_by($orderby, $direction = '')
{
$direction = (in_array(strtoupper(trim($direction)), array('ASC', 'DESC'), TRUE))? ' '.$direction : ' ASC';
$this->ar_orderby[] = $orderby.$direction;
return $this;
}
/**
* Runs the Query
*
*/
public function get()
{
$result = mysql_query($this->_compile_select(), $this->db) or die(mysql_error());
$this->_reset_select();
$this->_result = $result;
return $this;
}
/**
* Results as object
*
*/
public function result()
{
$aData = array();
while ($aRow = mysql_fetch_object($this->_result))
$aData[] = $aRow;
return $aData;
}
/**
* Results as array
*
*/
public function result_array()
{
$aData = array();
while ($aRow = mysql_fetch_array($this->_result, MYSQL_ASSOC))
$aData[] = $aRow;
return $aData;
}
/**
* Count Results
*
*/
public function count_all_results($table = '')
{
if ($table != '')
$this->from($table);
$sql = $this->_compile_select($this->_count_string . 'numrows');
$query = mysql_query($sql) or die(mysql_error());
$this->_reset_select();
$row = mysql_fetch_object($query);
return (int) $row->numrows;
}
/**
* Escape
*
*/
public function escape_db($text = "")
{
return mysql_real_escape_string($text);
}
/**
* Compile sql string
*
*/
protected function _compile_select($q = NULL)
{
$sql = ($q == NULL)? 'SELECT ' : $q ;
$sql .= implode(',', $this->ar_select);
if(count($this->ar_from) > 0)
$sql .= "\nFROM (".implode(',', $this->ar_from).")";
if (count($this->ar_join) > 0)
$sql .= "\n".implode("\n", $this->ar_join);
if (count($this->ar_where) > 0)
$sql .= "\nWHERE " . implode("\n", $this->ar_where);
if (count($this->ar_orderby) > 0)// check
{
$sql .= "\nORDER BY " . implode(', ', $this->ar_orderby);
if ($this->ar_order !== FALSE)
$sql .= ($this->ar_order == 'desc')? ' DESC' : ' ASC';
}
if (is_numeric($this->ar_limit))
$sql .= "\nLIMIT ".(($this->ar_offset == 0)? '' : $this->ar_offset.', ').$this->ar_limit;
return $sql;
}
/**
* Protect identifiers
*
*/
protected function _protect_identifiers($text)
{
$_pattern = '/\b(?<!"|\')(\w+)(?!\\1)\b/i';
$item = preg_replace('/[\t ]+/', ' ', $text);
$alias = '';
if (strpos($item, ' ') !== FALSE)
{
$alias = strstr($item, " ");
$item = substr($item, 0, - strlen($alias));
}
if (strpos($item, '(') !== FALSE)
return $item.$alias;
return preg_replace($_pattern, $this->_escape('$1'), $item).$alias;
}
/**
* Test Operator
*
*/
protected function _has_operator($str)
{
return (!preg_match("/(\s|<|>|!|=|is null|is not null)/i", trim($str)))? FALSE : TRUE;
}
/**
* Escape
*
*/
protected function _escape($text)
{
return $this->_escape_char . $text . $this->_escape_char ;
}
/**
* Reset arrays
*
*/
protected function _reset_select()
{
$ar_reset_items = array(
'ar_select' => array(),
'ar_from' => array(),
'ar_join' => array(),
'ar_where' => array(),
'ar_orderby' => array(),
'ar_limit' => FALSE,
'ar_offset' => FALSE,
'ar_order' => FALSE
);
foreach ($ar_reset_items as $item => $default_value)
$this->$item = $default_value;
}
}
/* End of file ActiveRecords.php */
\ No newline at end of file
service/ActiveRecords/mysql2.php 0 → 100755
View file @ 68574d69
<?php
/**
* Ignited Datatables ActiveRecords library for MySql
*
* @subpackage libraries
* @category library
* @version 0.1
* @author Yusuf Ozdemir <yusuf@ozdemir.be>
*/
class ActiveRecords
{
/**
* Variables
*
*/
var $ar_select = array();
var $ar_from = array();
var $ar_join = array();
var $ar_where = array();
var $ar_orderby = array();
var $ar_limit = FALSE;
var $ar_offset = FALSE;
var $ar_order = FALSE;
var $_escape_char = '`';
var $_count_string = 'SELECT COUNT(*) AS ';
var $username = 'root';
var $password = '';
var $database = '';
var $hostname = 'localhost';
var $port = '';
var $db ;
var $_result;
/**
* Construct function
*
*/
public function connect($config)
{
foreach ($config as $key => $val)
if(in_array($key, array('hostname', 'username', 'password', 'database', 'port')))
$this->$key = $val;
$this->db_connect();
$this->db_select();
}
/**
* DB connection
*
*/
protected function db_connect()
{
if ($this->port != '')
$this->hostname .= ':'.$this->port;
$this->db = @mysql_connect($this->hostname, $this->username, $this->password, TRUE);
}
/**
* DB Select
*
*/
protected function db_select()
{
@mysql_select_db( $this->database, $this->db ) or
die( 'Could not select database ' . $this->database );
}
/**
* Generates the SELECT portion of the query
*
*/
public function select($columns, $backtick_protect = TRUE)
{
foreach ($columns as $column)
$this->ar_select[] = ($backtick_protect == TRUE)? $this->_protect_identifiers(trim($column)) : trim($column);
return $this;
}
/**
* Generates the FROM portion of the query
*
*/
public function from($from)
{
foreach ((array)$from as $f)
$this->ar_from[] = $this->_protect_identifiers(trim($f));
return $this;
}
/**
* Generates the JOIN portion of the query
*
*/
public function join($table, $cond, $type = '')
{
if ($type != '')
{
$type = strtoupper(trim($type));
$type = (!in_array($type, array('LEFT', 'RIGHT', 'OUTER', 'INNER', 'LEFT OUTER', 'RIGHT OUTER')))? '':$type.' ' ;
}
$join = $type.'JOIN '.$this->_protect_identifiers($table).' ON '.$this->_protect_identifiers($cond);
$this->ar_join[] = $join;
return $this;
}
/**
* Generates the WHERE portion of the query
*
*/
public function where($key, $value = NULL, $escape = TRUE, $type = 'AND ')
{
if ( ! is_array($key))
$key = array($key => $value);
foreach ($key as $k => $v)
{
$prefix = (count($this->ar_where) == 0)? '' : $type;
if($v != NULL)
{
if($k=="genelist_pfam.genelist_pfam_id like" || $k=="syno2.field2 like" || $k=="description like" || $k=="name_space like" || $k=="genelist_panther.genelist_panther_id like" ){
$k = ($this->_has_operator($k) == TRUE)? $k : $k . ' =';
$v = ($escape == TRUE)? ' "' . $v . '" ' : $v;
}else{
$k = ($this->_has_operator($k) == TRUE)? $k : $k . ' =';
$v = ($escape == TRUE)? ' ("' . $v . '")' : $v;
}
}
$this->ar_where[] = $prefix . (($escape == TRUE)? $this->_protect_identifiers($k.$v) : $k.$v);
}
return $this;
}
/**
* Generates the LIMIT portion of the query
*
*/
public function limit($value, $offset = '')
{
$this->ar_limit = $value;
if ($offset != '')
$this->ar_offset = $offset;
return $this;
}
/**
* Generates the ORDER BY portion of the query
*
*/
public function order_by($orderby, $direction = '')
{
$direction = (in_array(strtoupper(trim($direction)), array('ASC', 'DESC'), TRUE))? ' '.$direction : ' ASC';
$this->ar_orderby[] = $orderby.$direction;
return $this;
}
/**
* Runs the Query
*
*/
public function get()
{
$result = mysql_query($this->_compile_select(), $this->db) or die(mysql_error());
$this->_reset_select();
$this->_result = $result;
return $this;
}
/**
* Results as object
*
*/
public function result()
{
$aData = array();
while ($aRow = mysql_fetch_object($this->_result))
$aData[] = $aRow;
return $aData;
}
/**
* Results as array
*
*/
public function result_array()
{
$aData = array();
while ($aRow = mysql_fetch_array($this->_result, MYSQL_ASSOC))
$aData[] = $aRow;
return $aData;
}
/**
* Count Results
*
*/
public function count_all_results($table = '')
{
if ($table != '')
$this->from($table);
$sql = $this->_compile_select($this->_count_string . 'numrows');
$query = mysql_query($sql) or die(mysql_error());
$this->_reset_select();
$row = mysql_fetch_object($query);
return (int) $row->numrows;
}
/**
* Escape
*
*/
public function escape_db($text = "")
{
return mysql_real_escape_string($text);
}
/**
* Compile sql string
*
*/
protected function _compile_select($q = NULL)
{
$sql = ($q == NULL)? 'SELECT ' : $q ;
$sql .= implode(',', $this->ar_select);
if(count($this->ar_from) > 0)
$sql .= "\nFROM (".implode(',', $this->ar_from).")";
if (count($this->ar_join) > 0)
$sql .= "\n".implode("\n", $this->ar_join);
if (count($this->ar_where) > 0)
$sql .= "\nWHERE " . implode("\n", $this->ar_where);
if (count($this->ar_orderby) > 0)// check
{
$sql .= "\nORDER BY " . implode(', ', $this->ar_orderby);
if ($this->ar_order !== FALSE)
$sql .= ($this->ar_order == 'desc')? ' DESC' : ' ASC';
}
if (is_numeric($this->ar_limit))
$sql .= "\nLIMIT ".(($this->ar_offset == 0)? '' : $this->ar_offset.', ').$this->ar_limit;
//echo $sql;
return $sql;
}
/**
* Protect identifiers
*
*/
protected function _protect_identifiers($text)
{
$_pattern = '/\b(?<!"|\')(\w+)(?!\\1)\b/i';
$item = preg_replace('/[\t ]+/', ' ', $text);
$alias = '';
if (strpos($item, ' ') !== FALSE)
{
$alias = strstr($item, " ");
$item = substr($item, 0, - strlen($alias));
}
if (strpos($item, '(') !== FALSE)
return $item.$alias;
return preg_replace($_pattern, $this->_escape('$1'), $item).$alias;
}
/**
* Test Operator
*
*/
protected function _has_operator($str)
{
return (!preg_match("/(\s|<|>|!|=|is null|is not null)/i", trim($str)))? FALSE : TRUE;
}
/**
* Escape
*
*/
protected function _escape($text)
{
return $this->_escape_char . $text . $this->_escape_char ;
}
/**
* Reset arrays
*
*/
protected function _reset_select()
{
$ar_reset_items = array(
'ar_select' => array(),
'ar_from' => array(),
'ar_join' => array(),
'ar_where' => array(),
'ar_orderby' => array(),
'ar_limit' => FALSE,
'ar_offset' => FALSE,
'ar_order' => FALSE
);
foreach ($ar_reset_items as $item => $default_value)
$this->$item = $default_value;
}
}
/* End of file ActiveRecords.php */
\ No newline at end of file
service/ActiveRecords/mysqli.php 0 → 100755
View file @ 68574d69
<?php
/**
* Ignited Datatables ActiveRecords library for MySqli
*
* @subpackage libraries
* @category library
* @version 0.1
* @author Yusuf Ozdemir <yusuf@ozdemir.be>
*/
class ActiveRecords
{
/**
* Variables
*
*/
var $ar_select = array();
var $ar_from = array();
var $ar_join = array();
var $ar_where = array();
var $ar_orderby = array();
var $ar_limit = FALSE;
var $ar_offset = FALSE;
var $ar_order = FALSE;
var $_escape_char = '`';
var $_count_string = 'SELECT COUNT(*) AS ';