Merge branch 'prerelease' into improvement/LIMS-77/link-lab-contact-t…

…o-fedids

.github/pull_request_template.md

@@ -0,0 +1,13 @@
+**NOTE**: (PR title should be of the form ticket:short description, e.g. TICKET-123: Add more templates)
+
+**JIRA ticket**: [TICKET-123](https://link.to.jira)
+
+**Summary**:
+
+A brief description of what this pull request aims to achieve
+
+**Changes**:
+- List changes made in this pull request
+
+**To test**:
+- List actions that should be taken to test that functionality works as expected

.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

api/assets/emails/dewar-transfer.html

@@ -5,16 +5,7 @@
 
 Dear local contact: <?php echo $data['LOCALCONTACT'] ?> <?php echo $data['LCEMAIL'] ?>,
 
-Your user: <?php echo $data['GIVENNAME'] ?> <?php echo $data['FAMILYNAME'] ?> requested an internal transfer for his/her dewar(s). Please print this e-mail and affix it on the shipping case and put the dewar for the visit <?php echo $data['VISIT'] ?> on the rack outside the beamline: "to be Stored at Diamond" by the <?php echo $data['DELIVERYAGENT_SHIPPINGDATE'] ?>.
-
-Local contact for next visit: <?php echo $data['NEXTLOCALCONTACT'] ?> <?php echo $data['LCNEXTEMAIL'] ?>
-
-
-Dear EHC,
-
-Please collect the dewar from visit <?php echo $data['VISIT'] ?> <?php if($data['FACILITYCODE']): ?>(Dewar Code: <?php echo $data['FACILITYCODE'] ?>)<?php endif; ?> currently stored on the rack outside <?php echo $data['LOCATION'] ?> and transfer it to the <?php echo $data['NEXTLOCATION'] ?> rack in the MX storage room
-The dewar should be ready for internal transfer by the <?php echo $data['DELIVERYAGENT_SHIPPINGDATE'] ?>
-
+Your user: <?php echo $data['GIVENNAME'] ?> <?php echo $data['FAMILYNAME'] ?> from visit <?php echo $data['VISIT'] ?> requested an internal transfer for his/her dewar(s). Please print this e-mail and affix it on the shipping case.
 
 Information for the transfer: 
 
@@ -42,14 +33,11 @@
 Current dewar location
 <?php echo $data['LOCATION'] ?>
 
-New Location in storage room
-<?php echo $data['NEXTLOCATION'] ?>
-
-Pickup date:
-<?php echo $data['DELIVERYAGENT_SHIPPINGDATE'] ?>
-
 Local contact email (in case of problems finding the dewar):
 <?php echo $data['LOCALCONTACT'] ?> <?php echo $data['LCEMAIL'] ?>
 
+Local contact for next visit:
+<?php echo $data['NEXTLOCALCONTACT'] ?> <?php echo $data['LCNEXTEMAIL'] ?>
+
 Comments:
 <?php echo $data['COMMENTS'] ?>

api/assets/emails/html/dewar-transfer.html

@@ -3,16 +3,9 @@ <h1 style="font-size: 16px; font-weight: normal; border-bottom: 1px solid #000;
 
 		<div class="inset" style="margin: 1%; padding: 1%; margin-bottom: 2%; border-radius: 5px; background: #82d180">
 			<h2>Local Contact: <?php echo $data['LOCALCONTACT'] ?> <?php echo $data['LCEMAIL'] ?></h2>
-			<p><?php echo $data['GIVENNAME'] ?> <?php echo $data['FAMILYNAME'] ?> requested an internal transfer for his/her dewar(s). Please print this e-mail and affix it on the shipping case and put the dewar for the visit <?php echo $data['VISIT'] ?> on the rack outside the beamline: "to be Stored at Diamond" by the <?php echo $data['DELIVERYAGENT_SHIPPINGDATE'] ?></p>
-			<p>Local contact for next visit: <?php echo $data['NEXTLOCALCONTACT'] ?> <?php echo $data['LCNEXTEMAIL'] ?></p>
+			<p><?php echo $data['GIVENNAME'] ?> <?php echo $data['FAMILYNAME'] ?> from visit <?php echo $data['VISIT'] ?> requested an internal transfer for his/her dewar(s). Please print this e-mail and affix it on the shipping case.</p>
 		</div>
 
-		<div class="inset" style="margin: 1%; padding: 1%; margin-bottom: 2%; border-radius: 5px; background: #82d180">
-			<h2>EHCs</h2>
-			<p>Please collect the dewar from visit <?php echo $data['VISIT'] ?> <?php if($data['FACILITYCODE']): ?>(Dewar Code: <?php echo $data['FACILITYCODE'] ?>)<?php endif; ?> currently stored on the rack outside <?php echo $data['LOCATION'] ?> and transfer it to the <?php echo $data['NEXTLOCATION'] ?> rack in the MX storage room</p>
-			<p>The dewar should be ready for internal transfer by the <?php echo $data['DELIVERYAGENT_SHIPPINGDATE'] ?></p>
-		</div>
-
 		<table class="details" style="background: #f4f4f4; margin: 1%">
 			<tbody>
 				<?php if ($data['FACILITYCODE']): ?>
@@ -40,11 +33,10 @@ <h2>EHCs</h2>
 					<td><?php echo $data['NEXTVISIT'] ?></td>
 				</tr>
 				<tr>
-					<td style="padding: 1.5%; font-weight: bold">New Location</td>
-					<td><?php echo $data['NEXTLOCATION'] ?></td>
+					<td style="padding: 1.5%; font-weight: bold">New Local Contact</td>
+					<td><?php echo $data['NEXTLOCALCONTACT'] ?></td>
 				</tr>
 
-
 				<tr>
 					<td style="padding: 1.5%; font-weight: bold">Full Name</td>
 					<td><?php echo $data['GIVENNAME'] ?> <?php echo $data['FAMILYNAME'] ?></td>
@@ -61,12 +53,7 @@ <h2>EHCs</h2>
 					<td style="padding: 1.5%; font-weight: bold">Lab / Company Name</td>
 					<td><?php echo $data['LABNAME'] ?></td>
 				</tr>
-
-				<tr>
-					<td style="padding: 1.5%; font-weight: bold">Pickup Date</td>
-					<td><?php echo $data['DELIVERYAGENT_SHIPPINGDATE'] ?></td>
-				</tr>
-
+
 				<tr>
 					<td style="padding: 1.5%; font-weight: bold">Comments</td>
 					<td><?php echo nl2br($data['COMMENTS']) ?></td>

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
@@ -242,6 +247,7 @@
 
     # Shipping service details
     $use_shipping_service = null;
+    $use_shipping_service_incoming_shipments = null;
     $shipping_service_url = null;
     $shipping_service_links_in_emails = null;
 

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']);
     });

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");

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($databaseConnectionFactory)
@@ -19,25 +20,28 @@ function __construct($databaseConnectionFactory)
 
     private $databaseConnectionFactory;
 
-    public function get()
-    {
-        // Global variable is named $dbtype in config.php.
+    public function get($databaseType = null)
+    {   
         global $dbtype;
-        $database_type = $dbtype;
+
+        if ( $databaseType == null) {
+            // Global variable is named $dbtype in config.php.
+            $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';
+            $databaseType = '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)) {
+            $selectedDBConfig = $this->database_types[strtolower($databaseType)];
 
-            $full_class_name = 'SynchWeb\\Database\\Type\\' . $dbClassName;
+            $full_class_name = 'SynchWeb\\Database\\Type\\' . $selectedDBConfig["dbClassName"];
 
             if (class_exists($full_class_name)) {
-                $conn = $this->databaseConnectionFactory->get($dbClassName);
+                $conn = $this->databaseConnectionFactory->get($selectedDBConfig["dataConnectionName"]);
                 return new $full_class_name($conn);
             }
             else {
@@ -46,7 +50,7 @@ public function get()
 
         }
         else {
-            error_log("Database type '$database_type' not configured.");
+            error_log("Database type '$databaseType' not configured.");
         }
         return null;
     }

api/src/Database/DatabaseQueryBuilder.php

@@ -24,8 +24,11 @@ class DatabaseQueryBuilder
     private $query_bound_values = [];
     /** @var ?string where clause column name */
     private $where_columnName = Null;
-    /** @var ?mixed where vlause value */
+    /** @var ?mixed where clause value */
     private $where_value = Null;
+    /** @var array join clauses*/
+    private $join_clauses = [];
+
     /**
      * @var DatabaseParent database parent to use
      */
@@ -104,6 +107,33 @@ public function insert($expectedTable)
         return $this->db->id();
     }
 
+
+    /** 
+     * Add while join clauses with no processing except to remove duplicates
+     * ONLY USED WITH getJoins at the moment
+     * 
+     * @param string $join_clause The join clause to add, e.g. JOIN table t ON t.id = s.id
+     * @return DatabaseQueryBuilder the builder
+     */
+    public function joinClause($join_clause) 
+    {
+        if (!in_array($join_clause, $this->join_clauses))
+            array_push($this->join_clauses, $join_clause);
+        return $this;
+    }
+
+    /**
+     * Pull back the join clauses ready to be added to a SQL statement
+     * 
+     * This is a half-way house into adding join caluses to this builder
+     * 
+     * @return string The join caluses as one long string
+     */
+    public function getJoins()
+    {
+        return implode(" ", $this->join_clauses);
+    }
+
     private function bindArrayAsList($values): string
     {
         $bound_list_sql = "";

api/src/Database/Type/MySQL.php

@@ -202,6 +202,7 @@ class MySQL extends DatabaseParent {
         // Xray Centring
         'XrayCentring',
         'XrayCentringResult',
+        'XrayCentring',
 
         'BeamCalendar',
         'SpaceGroup',