Merge pull request #642 from DiamondLightSource/pre-release/2023-R3.3

Pre release/2023 r3.3
DiamondLightSource · Aug 15, 2023 · d0df7be · d0df7be
2 parents 5f7083b + 8415438
commit d0df7be
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Showing 34 changed files with 16,394 additions and 55 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -72,11 +72,16 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v3
 
+      - name: Use Node.js 18
+        uses: actions/setup-node@v3
+        with:
+          node-version: 18.x
       - name: JavaScript build, lint and test
         working-directory: ./client
         # hack the output from the linting steps to avoid these stopping the builds - we are not going to get 
         # to a clean output without considerable effort, but it's useful to see the output
         run: |
+              node --version
               npm ci
               npm run build
               npm run test

diff --git a/api/config_sample.php b/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

diff --git a/api/index.php b/api/index.php
@@ -69,7 +69,7 @@ function setupApplication($mode): Slim
         global $motd, $authentication_type, $cas_url, $cas_sso, $sso_url, $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' => $motd,
@@ -87,7 +87,8 @@ function setupApplication($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 $app;
@@ -102,6 +103,13 @@ function setupDependencyInjectionContainer($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']);
     });

diff --git a/api/src/Authentication/Type/OIDC.php b/api/src/Authentication/Type/OIDC.php
@@ -19,16 +19,18 @@ function __construct() {
         curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
         $response = curl_exec($ch);
         curl_close($ch);
-
         $newProviderConfig = json_decode($response);
-        $newProviderConfig->b64ClientCreds = base64_encode(
-            $oidc_client_id . ":" . $oidc_client_secret
-        );
 
-        if($newProviderConfig == null) {
+        if(!$newProviderConfig
+            || !isset($newProviderConfig->userinfo_endpoint)
+            || !isset($newProviderConfig->authorization_endpoint) 
+            || !isset($newProviderConfig->token_endpoint)) {
             error_log("OIDC Authentication provider replied with invalid JSON body");
             return;
         }
+        $newProviderConfig->b64ClientCreds = base64_encode(
+            $oidc_client_id . ":" . $oidc_client_secret
+        );
 
         $this->providerConfig = $newProviderConfig;
     }
@@ -43,9 +45,12 @@ private function getUser($token)
         $response = curl_exec($ch);
         curl_close($ch);
 
-        $fedid = json_decode($response)->id;
+        $response_json = json_decode($response);
+        if (!$response_json || !isset($response_json->id)) {
+            return false;
+        }
 
-        return $fedid;
+        return $response_json->id;
     }
 
     function authenticate($login, $password) 
@@ -92,8 +97,14 @@ function authenticateByCode($code)
         curl_setopt($ch, CURLOPT_HTTPHEADER, array('Authorization: Basic ' . $this->providerConfig->b64ClientCreds));
         $response = curl_exec($ch);
         curl_close($ch);
-
-        $token = json_decode($response)->access_token;
+
+        $response_json = json_decode($response);
+        if (!$response_json || !isset($response_json->access_token)) {
+            error_log("Invalid authentication attempt, provider returned invalid response");
+            return false;
+        }        
+
+        $token = $response_json->access_token;
 
         if(!$token) {
             error_log("Invalid authentication attempt, provider returned no access token");

diff --git a/api/src/Database/DatabaseConnectionFactory.php b/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.");

diff --git a/api/src/Database/DatabaseFactory.php b/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;
     }

diff --git a/api/src/Database/Type/MySQL.php b/api/src/Database/Type/MySQL.php
@@ -200,6 +200,7 @@ class MySQL extends DatabaseParent {
         'PhasingProgramAttachment',
 
         // Xray Centring
+        'XrayCentring',
         'XrayCentringResult',
 
         'BeamCalendar',
@@ -551,4 +552,4 @@ function close()
         if ($this->conn)
             $this->conn->close();
     }   
-}
+}