LIMS-116: Summary page revamp

api/config_sample.php

@@ -13,6 +13,11 @@
     $isb  = array('user' => 'user', 'pass' => 'pass', 'db' => 'localhost/ispyb');
     $dbtype = 'mysql';
 
+    # Summary Database credentials 
+    ######### DELETE if not using connection. 
+    $summarydbconfig = array('user' => 'user', 'pass' => 'pass', 'db' => 'localhost/ispyb');
+    $ifsummary = true;
+
     # Encoded JWT key, used to sign and check validaty of jwt tokens
     # - Create one of these using /api/authenticate/key
     #   This can be changed to invalidate all currently active tokens

api/index.php

@@ -69,7 +69,7 @@ function setupApplication($mode): Slim
         global $motd, $authentication_type, $cas_url, $cas_sso, $package_description,
             $facility_courier_countries, $facility_courier_countries_nde,
             $dhl_enable, $dhl_link, $scale_grid, $scale_grid_end_date, $preset_proposal, $timezone,
-            $valid_components, $enabled_container_types;
+            $valid_components, $enabled_container_types, $ifsummary;
         $app->contentType('application/json');
         $app->response()->body(json_encode(array(
             'motd' => $motd,
@@ -86,7 +86,8 @@ function setupApplication($mode): Slim
             'preset_proposal' => $preset_proposal,
             'timezone' => $timezone,
             'valid_components' => $valid_components,
-            'enabled_container_types' => $enabled_container_types
+            'enabled_container_types' => $enabled_container_types,
+            'ifsummary' => $ifsummary
         )));
     });
     return $app;
@@ -101,6 +102,13 @@ function setupDependencyInjectionContainer($app)
         return $db;
     });
 
+    $app->container->singleton('dbsummary', function () use ($app): DatabaseParent {
+        $dbFactory = new DatabaseFactory(new DatabaseConnectionFactory());
+        $db = $dbFactory->get("summary");
+        $db->set_app($app);
+        return $db;
+    });
+
     $app->container->singleton('authData', function () use ($app) {
         return new AuthenticationData($app->container['db']);
     });

api/src/Database/DatabaseConnectionFactory.php

@@ -9,6 +9,7 @@ class DatabaseConnectionFactory
     public function get($databaseType)
     {
         global $isb;
+        global $summarydbconfig;
 
         if (!$databaseType) {
             error_log('Database type variable, dbtype, is not specified in config.php - defaulting to MySql.');
@@ -24,6 +25,16 @@ public function get($databaseType)
             $conn = new \mysqli($host, $isb['user'], $isb['pass'], $dbn, $port);
             $conn->set_charset("utf8mb4");
         }
+        elseif ($databaseType == 'PureMySQL') {
+            $port = array_key_exists('port', $summarydbconfig) ? $summarydbconfig['port'] : null;
+            if (!$port) {
+                $port = ini_get("mysqli.default_port");
+            }
+            list($host, $dbn) = explode('/', $summarydbconfig['db']);
+            $conn = new \mysqli($host, $summarydbconfig['user'], $summarydbconfig['pass'], $dbn, $port);
+            $conn->set_charset("utf8mb4");
+        }
+
 
         if ($conn == null) {
             Utils::returnError("Database Configuration Error", "Database connection for type '$databaseType' does not exist.");

api/src/Database/DatabaseFactory.php

@@ -9,7 +9,8 @@ class DatabaseFactory
     // Value is class name in SynchWeb\Database\Type namespace.
     // Key is lower case representation of class name.
     public $database_types = array(
-        'mysql' => 'MySQL'
+        'mysql' => ["dbClassName" =>'MySQL', "dataConnectionName" => 'MySQL'],
+        'summary' => ["dbClassName" =>'PureMySQL', "dataConnectionName" => 'PureMySQL']
     );
 
     function __construct($databaseConnectionFactory)
@@ -19,25 +20,27 @@ function __construct($databaseConnectionFactory)
 
     private $databaseConnectionFactory;
 
-    public function get()
-    {
-        // Global variable is named $dbtype in config.php.
-        global $dbtype;
-        $database_type = $dbtype;
+    public function get($databaseType = null)
+    {   
+        if ( $databaseType == null) {
+            // Global variable is named $dbtype in config.php.
+            global $dbtype;
+            $databaseType = $dbtype;
+        }
 
-        if (!$database_type) {
+        if (!$databaseType) {
             error_log('Database type variable, dbtype, is not specified in config.php - defaulting to MySql.');
             $database_type = 'MySQL';
         }
 
         // Determine fully-qualified class name of database class corresponding to $database_type.
-        if (key_exists(strtolower($database_type), $this->database_types)) {
-            $dbClassName = $this->database_types[strtolower($database_type)];
+        if (key_exists(strtolower($databaseType), $this->database_types)) {
+            $dbType = $this->database_types[strtolower($databaseType)];
 
-            $full_class_name = 'SynchWeb\\Database\\Type\\' . $dbClassName;
+            $full_class_name = 'SynchWeb\\Database\\Type\\' . $dbType["dbClassName"];;
 
             if (class_exists($full_class_name)) {
-                $conn = $this->databaseConnectionFactory->get($dbClassName);
+                $conn = $this->databaseConnectionFactory->get($dbType["dataConnectionName"]);
                 return new $full_class_name($conn);
             }
             else {
@@ -46,7 +49,7 @@ public function get()
 
         }
         else {
-            error_log("Database type '$database_type' not configured.");
+            error_log("Database type '$databaseType' not configured.");
         }
         return null;
     }

api/src/Database/Type/PureMySQL.php

@@ -0,0 +1,262 @@
+<?php
+
+namespace SynchWeb\Database\Type;
+
+use SqlFormatter;
+use SynchWeb\Database\DatabaseParent;
+
+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 $errors = 0;
+
+
+    function __construct($conn)
+    {
+        parent::__construct($conn);
+
+        mysqli_report(MYSQLI_REPORT_ERROR | MYSQLI_REPORT_STRICT); // throw exceptions.
+
+        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
+    }
+
+    function start_transaction()
+    {
+        $this->transaction = True;
+        $this->conn->autocommit(False);
+    }
+
+    function end_transaction()
+    {
+        if ($this->errors > 0)
+            $this->conn->rollback();
+        else
+            $this->conn->commit();
+
+        $this->conn->autocommit(True);
+        $this->transaction = False;
+
+        if ($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);
+    }
+
+
+
+    // 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+/', ' ', $sql); // remove excess spaces
+    }
+
+    function pq($query, $args = array(), $upperCaseKeys = true)
+    {
+
+        if ($this->debug)
+        {
+            print '<h1 class="debug">MySQL Debug</h1>';
+            print SqlFormatter::format($query);
+            echo '<br/>';
+        }
+
+        $stmt = $this->conn->prepare($query);
+
+        if (!$stmt)
+        {
+            if ($this->transaction)
+                $this->errors++;
+            else
+            {
+                $err = mysqli_error($this->conn);
+                $this->error('There was an error with MySQL', $err);
+                return;
+            }
+        }
+
+        if (sizeof($args))
+        {
+            $vtypes = array('NULL' => 'i', 'integer' => 'i', 'double' => 'd', 'string' => 's');
+
+            $strfs = '';
+            foreach ($args as $a)
+            {
+                $t = gettype($a);
+                $strfs .= $vtypes[$t];
+            }
+
+            array_unshift($args, $strfs);
+            call_user_func_array(array(&$stmt, 'bind_param'), $this->refs($args));
+        }
+
+        $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, $c);
+                    }
+                }
+            }
+        }
+
+        if ($this->debug)
+        {
+            echo '<br/>';
+            print_r('row count: ' . sizeof($data));
+            echo '<br/>';
+        }
+
+        // Need mysqlnd for this :(
+        // $result = $stmt->get_result();
+
+        // $data = array();
+
+        // if ($result) {
+        //     if($result->num_rows > 0) {
+        //         while($row = $result->fetch_assoc()) {
+        //             array_push($data, array_change_key_case($row, CASE_UPPER));
+        //         }
+        //     }
+        // }
+
+        $stmt->close();
+
+        return $data;
+    }
+
+    // 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);
+        }
+
+        $union = implode("\n$union_kw\n", $queries);
+        if ($wrapper)
+        {
+            $union = preg_replace('/:QUERY/', $union, $wrapper);
+        }
+
+        return $this->pq($union, $all_args);
+    }
+
+    private function refs($arr)
+    {
+        $refs = array();
+        foreach ($arr as $key => $value)
+        {
+            $refs[$key] = & $arr[$key];
+        }
+        return $refs;
+    }
+
+    function read($field)
+    {
+        return $field;
+    }
+
+    function id()
+    {
+        return mysqli_insert_id($this->conn);
+    }
+
+    function close()
+    {
+        if ($this->conn)
+            $this->conn->close();
+    }   
+}