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LIMS-116: Summary page revamp (#606)
* updating .gitignore * adding frontend files and building backend * adding front end files and router files * create sidebar, filter options added, routes added * add routing to page,search bar and column selector * adding pagination continutation * adding csv, all columns, rest of filters * added descending and ascending * sidebar dropdown&changed data structure&hide row * cleaning up fixing jump bug * refactored backend mapped data * added expanding row * refactored favourites * refactored orderby filter * cleaned up code, added comments * added all params to watcher * added summary db connection * add routes to summary * add backend changes summarypage * changes to expandable sidebar, cleaning up fronte * clean up, add functions to get data * front end changes, group concat backend * remove summarypage code * fix pagination, timeout * delete old summary file * changed pagination in summary.php * changed backend to not include tot * fix refined cell c column * added ifsets to avoid undefined offset error * delete offset for output * change order of operands * change filters, fix operands * fix csv button * changed prop to propid * format beamlinename * change al,be,gamma * add selected columns summary * additional changes for selected columns * add multiple selections change expandable sidebar * redo routing, keep alive summary * fixes, change routing, results display, orderby * fixes to selected columns * format page to allow for customisation * area for potential formatting and fix to querypara * changes to regex, combobox multiple, and fomat * column select fix, resize pill fix, format inputs * Update api/src/Database/DatabaseConnectionFactory.php Co-authored-by: Guilherme Francisco <[email protected]> * Update client/src/js/modules/types/sp/menu.js Co-authored-by: Guilherme Francisco <[email protected]> * Update client/src/js/modules/types/saxs/menu.js Co-authored-by: Guilherme Francisco <[email protected]> * Update client/src/js/modules/types/pow/menu.js Co-authored-by: Guilherme Francisco <[email protected]> * Update client/src/js/modules/types/mx/menu.js Co-authored-by: Guilherme Francisco <[email protected]> * Update client/src/js/modules/types/em/menu.js Co-authored-by: Guilherme Francisco <[email protected]> * Update client/src/js/app/components/combo-box.vue Co-authored-by: Guilherme Francisco <[email protected]> * Update api/src/Database/DatabaseFactory.php Co-authored-by: John Holt <[email protected]> * Update api/src/TemplateParser.php Co-authored-by: Guilherme Francisco <[email protected]> * Code review changes: database conns, code tidy * add get started button --------- Co-authored-by: Guilherme Francisco <[email protected]> Co-authored-by: John Holt <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,262 @@ | ||
| <?php | ||
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| namespace SynchWeb\Database\Type; | ||
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| use SqlFormatter; | ||
| use SynchWeb\Database\DatabaseParent; | ||
|
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| class PureMySQL extends DatabaseParent { | ||
| /** @var string */ | ||
| protected $type = 'mysql'; | ||
| /** @var string */ | ||
| private $lastQuery = ''; // provide a way of retrieving the last query run - by storing the data - can then call getLastQuery() - primarily for testing | ||
| /** @var array */ | ||
| private $lastArgs = array(); | ||
| /** @var bool */ | ||
| private $transaction = False; | ||
| /** @var int */ | ||
| private $errors = 0; | ||
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|
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| function __construct($conn) | ||
| { | ||
| parent::__construct($conn); | ||
|
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| mysqli_report(MYSQLI_REPORT_ERROR | MYSQLI_REPORT_STRICT); // throw exceptions. | ||
|
|
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| if (mysqli_connect_errno()) | ||
| { | ||
| $this->error('There was an error connecting to MySQL: ', htmlentities(mysqli_connect_errno())); | ||
| } | ||
| } | ||
|
|
||
| // wsrep_sync_wait waits for cluster replication on a mariadb cluster | ||
| function wait_rep_sync($state = false) | ||
| { | ||
| # Empty - DatabaseFactory checks this exists | ||
| } | ||
|
|
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| function start_transaction() | ||
| { | ||
| $this->transaction = True; | ||
| $this->conn->autocommit(False); | ||
| } | ||
|
|
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| function end_transaction() | ||
| { | ||
| if ($this->errors > 0) | ||
| $this->conn->rollback(); | ||
| else | ||
| $this->conn->commit(); | ||
|
|
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| $this->conn->autocommit(True); | ||
| $this->transaction = False; | ||
|
|
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| if ($this->errors > 0) | ||
| $this->error('There was an error with MySQL', $this->conn->error . __LINE__); | ||
| $this->errors = 0; | ||
| } | ||
|
|
||
| function paginate($query, $args = array()) | ||
| { | ||
| // MySQL is Limit Start Row, Number | ||
| // Oracle subselect is Start Row, End Row | ||
| if (sizeof($args)) | ||
| $args[sizeof($args) - 1] = $args[sizeof($args) - 1] - $args[sizeof($args) - 2]; | ||
| return $this->pq("$query LIMIT ?,?", $args); | ||
| } | ||
|
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|
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|
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| // return the last SQL query executed in fully expanded form (i.e. including binded params) - this is mainly for testing purposes (so ideally would not be part of the actual class...) | ||
| function getLastQuery() | ||
| { | ||
| echo '<br/>'; | ||
| $sql = $this->lastQuery; | ||
| for ($i = 1; $i < count($this->lastArgs); $i++) | ||
| { | ||
| $val = $this->lastArgs[$i]; | ||
| if (is_string($val)) | ||
| { | ||
| $val = "'" . $val . "'"; | ||
| } | ||
| else if (is_null($val)) | ||
| { | ||
| $val = 'null'; | ||
| } | ||
| $sql = preg_replace('/\?/', $val, $sql, 1); | ||
| } | ||
| $sql = preg_replace('/\\n/', '', $sql); // replace newlines | ||
| return preg_replace('/\s\s+/', ' ', $sql); // remove excess spaces | ||
| } | ||
|
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| function pq($query, $args = array(), $upperCaseKeys = true) | ||
| { | ||
|
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| if ($this->debug) | ||
| { | ||
| print '<h1 class="debug">MySQL Debug</h1>'; | ||
| print SqlFormatter::format($query); | ||
| echo '<br/>'; | ||
| } | ||
|
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| $stmt = $this->conn->prepare($query); | ||
|
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| if (!$stmt) | ||
| { | ||
| if ($this->transaction) | ||
| $this->errors++; | ||
| else | ||
| { | ||
| $err = mysqli_error($this->conn); | ||
| $this->error('There was an error with MySQL', $err); | ||
| return; | ||
| } | ||
| } | ||
|
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| if (sizeof($args)) | ||
| { | ||
| $vtypes = array('NULL' => 'i', 'integer' => 'i', 'double' => 'd', 'string' => 's'); | ||
|
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| $strfs = ''; | ||
| foreach ($args as $a) | ||
| { | ||
| $t = gettype($a); | ||
| $strfs .= $vtypes[$t]; | ||
| } | ||
|
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| array_unshift($args, $strfs); | ||
| call_user_func_array(array(&$stmt, 'bind_param'), $this->refs($args)); | ||
| } | ||
|
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| $this->lastQuery = $query; | ||
| $this->lastArgs = $args; | ||
| if ($this->debug) | ||
| { | ||
| print_r("Full SQL query: " . $this->getLastQuery()); | ||
| } | ||
|
|
||
| if (!$stmt->execute()) | ||
| { | ||
| if ($this->transaction) | ||
| $this->errors++; | ||
| else | ||
| { | ||
| $err = mysqli_error($this->conn); | ||
| $this->error('There was an error with MySQL', $err); | ||
| return; | ||
| } | ||
| } | ||
|
|
||
| $data = array(); | ||
| if (strpos($query, 'SELECT') !== false) | ||
| { | ||
| $result = $stmt->get_result(); | ||
| if ($result) | ||
| { | ||
| if ($result->num_rows > 0) | ||
| { | ||
| while ($row = $result->fetch_assoc()) | ||
| { | ||
| $c = array(); | ||
| // oracle inheritance ;( | ||
| foreach ($row as $key => $val) | ||
| { | ||
| if ($val !== null) | ||
| { | ||
| if (gettype($val) == gettype(0.1)) | ||
| $val = round($val, 5); | ||
| $val = strval($val); | ||
| } | ||
| if ($upperCaseKeys) | ||
| { | ||
| $key = strtoupper($key); | ||
| } | ||
| $c[$key] = $val; | ||
| } | ||
| array_push($data, $c); | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
|
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| if ($this->debug) | ||
| { | ||
| echo '<br/>'; | ||
| print_r('row count: ' . sizeof($data)); | ||
| echo '<br/>'; | ||
| } | ||
|
|
||
| // Need mysqlnd for this :( | ||
| // $result = $stmt->get_result(); | ||
|
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| // $data = array(); | ||
|
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| // if ($result) { | ||
| // if($result->num_rows > 0) { | ||
| // while($row = $result->fetch_assoc()) { | ||
| // array_push($data, array_change_key_case($row, CASE_UPPER)); | ||
| // } | ||
| // } | ||
| // } | ||
|
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| $stmt->close(); | ||
|
|
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| return $data; | ||
| } | ||
|
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||
| // Union multiple queries that take the same arguments and return the same columns | ||
| // Query can optionally be wrapped, where :QUERY will be replaced with the inner query: | ||
| // $wrapper = 'SELECT * FROM (:QUERY) GROUP BY id'; | ||
| function union($queries, $args, $all = false, $wrapper = null) | ||
| { | ||
| $nargs = sizeof($args); | ||
| $all_args = array(); | ||
| $union_kw = $all ? 'UNION ALL' : 'UNION'; | ||
| foreach ($queries as $i => &$query) | ||
| { | ||
| $offset = $i * $nargs; | ||
| $query = preg_replace_callback('/\:(\d+)/', | ||
| function ($mat) use ($offset) | ||
| { | ||
| return ':' . (intval($mat[1]) + $offset); | ||
| }, | ||
| $query); | ||
| $all_args = array_merge($all_args, $args); | ||
| } | ||
|
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| $union = implode("\n$union_kw\n", $queries); | ||
| if ($wrapper) | ||
| { | ||
| $union = preg_replace('/:QUERY/', $union, $wrapper); | ||
| } | ||
|
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| return $this->pq($union, $all_args); | ||
| } | ||
|
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| private function refs($arr) | ||
| { | ||
| $refs = array(); | ||
| foreach ($arr as $key => $value) | ||
| { | ||
| $refs[$key] = & $arr[$key]; | ||
| } | ||
| return $refs; | ||
| } | ||
|
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| function read($field) | ||
| { | ||
| return $field; | ||
| } | ||
|
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| function id() | ||
| { | ||
| return mysqli_insert_id($this->conn); | ||
| } | ||
|
|
||
| function close() | ||
| { | ||
| if ($this->conn) | ||
| $this->conn->close(); | ||
| } | ||
| } |
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