Merge remote-tracking branch 'origin/prerelease' into improvement/LIM…

…S-276/speed-up-get-all-containers-count

Use the sub sample sub select query from LIMS-452

.github/workflows/ci.yml

@@ -4,11 +4,13 @@ on:
   push:
     branches: 
       - 'master'
+      - 'prerelease'
       - 'release/**'
       - 'pre-release/**'
   pull_request:
     branches:
       - 'master'
+      - 'prerelease'
       - 'release/**'
       - 'pre-release/**'
 
@@ -54,7 +56,7 @@ jobs:
         with:
           bootstrap: api/vendor/autoload.php
           configuration: api/tests/phpunit.xml
-          php_extensions: xdebug mysqli
+          php_extensions: xdebug mysqli zip
           args: --coverage-text
           php_version: 7.3
           version: 9
@@ -70,11 +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

README.md

@@ -28,6 +28,12 @@ If not using the development VMs you will also need an instance of the
 ISPyB database - available
 [here](https://github.com/DiamondLightSource/ispyb-database).
 
+If not already installed, you must install the following packages:
+
+```
+php php-mysqlnd php-mbstring php-xml php-gd php-fpm php-cli php-xdebug
+```
+
 ### Check out the code
 ```sh
 $ git clone https://github.com/DiamondLightSource/SynchWeb

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

@@ -47,7 +47,10 @@ <h1 style="font-size: 16px; font-weight: normal; border-bottom: 1px solid #000;
 					<td>
 						<?php echo $data['GIVENNAME'] ?> <?php echo $data['FAMILYNAME'] ?><br />
 						<?php echo $data['LABNAME'] ?> <br />
-						<?php echo nl2br($data['ADDRESS']) ?>
+						<?php echo nl2br($data['ADDRESS']) ?> <br />
+						<?php echo $data['CITY'] ?> <br />
+						<?php echo $data['POSTCODE'] ?> <br />
+						<?php echo $data['COUNTRY'] ?>
 					</td>
 				</tr>
 				<tr>
@@ -60,7 +63,7 @@ <h1 style="font-size: 16px; font-weight: normal; border-bottom: 1px solid #000;
 					<td><?php echo $data['DELIVERYAGENT_AGENTNAME'] ?></td>
 				</tr>
 
-				<?php if (!$data['FACILITYCODE']): ?>
+				<?php if (!$data['TERMSACCEPTED']): ?>
 				<tr>
 					<td style="padding: 1.5%; font-weight: bold">Courier Account No.</td>
 					<td><?php echo $data['DELIVERYAGENT_AGENTCODE'] ?></td>

api/assets/pdf/visit_report.php

@@ -27,7 +27,7 @@
         <p>Registered Users</p>
         <ul>
             <?php foreach($users as $u): ?>
-                <li><?php echo $u['FULLNAME'] ?></li>
+                <li><?php echo $u['TITLE'] . ' ' . $u['GIVENNAME'] . ' ' . $u['FAMILYNAME'] ?></li>
             <?php endforeach; ?>
         </ul>
 

api/composer.json

@@ -19,7 +19,6 @@
     "firebase/php-jwt": "2.2.0",
     "jdorn/sql-formatter": "1.2.9",
     "mpdf/mpdf": "8.1.2",
-    "phpxmlrpc/phpxmlrpc": "3.1.2",
     "ralouphie/getallheaders": "2.0.5",
     "slim/slim": "2.6.2",
     "stomp-php/stomp-php": "3.0.6",

api/config_sample.php

@@ -13,20 +13,32 @@
     $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
     $jwt_key = '';
 
     # Auth type
-    # Can be cas, ldap
+    # Can be cas, ldap, oidc
     $authentication_type = 'cas';
 
     # CAS url (if using cas, assume https)
     $cas_url = 'cas.server.ac.uk';
 
     # Follow CAS SSO
     $cas_sso = true;
+    $sso_url = "sso.server.ac.uk";
+
+    # OIDC (or OAuth2) client ID and secret. Only useful if authentication_type is set to OIDC
+    $oidc_client_id = "oidcClientId";
+    $oidc_client_secret = "oidcClientSecret";
+    # Cookie key used for SSO/cookie based authentication
+    $cookie_key = "synchweb-auth";
 
     # CAS CA Cert (for SSO)
     $cacert = '/etc/certs/ca-bundle.crt';
@@ -52,6 +64,9 @@
     # Timezone
     $timezone = 'Europe/London';
 
+    # URL to access the PV archiver
+    $archive_url = '';
+
     # Valid Components
     #   Denotes that only staff may create proteins, otherwise they must come from replication 
     #   with a valid `externalid`, users may still clone proteins
@@ -144,6 +159,13 @@
     # and for shipment booked,
     $shipbooked_email = '[email protected]';
 
+    # dewar back in storage (complete)
+    $dewar_complete_email = '';
+
+    # Send a 'visit finished' email when a dewar moves from this beamline to this (regex) location
+    $dewar_complete_email_locations = array('i03' => '/tray-\w+/',
+                                           );
+
     # Industrial Contacts
     # - Industrial users get a personalised email with in contact details,
     #   template in assets/emails/dewar-stores-in-in.html
@@ -225,6 +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

@@ -66,16 +66,17 @@ function setupApplication($mode): Slim
     });
 
     $app->get('/options', function () use ($app) {
-        global $motd, $authentication_type, $cas_url, $cas_sso, $package_description,
+        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,
             'authentication_type' => $authentication_type,
             'cas_url' => $cas_url,
             'cas_sso' => $cas_sso,
+            'sso_url' => $sso_url,
             'package_description' => $package_description,
             'facility_courier_countries' => $facility_courier_countries,
             'facility_courier_countries_nde' => $facility_courier_countries_nde,
@@ -86,7 +87,8 @@ function setupApplication($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 $app;
@@ -101,6 +103,13 @@ function setupDependencyInjectionContainer($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/AuthenticationParent.php

@@ -12,4 +12,8 @@ interface AuthenticationInterface
     public function authenticate($login, $password);
 
     public function check();
+
+    public function authorise();
+
+    public function authenticateByCode($code);
 }

api/src/Authentication/AuthenticationTypeFactory.php

@@ -0,0 +1,54 @@
+<?php
+
+namespace SynchWeb\Authentication;
+
+class AuthenticationTypeFactory {
+
+    // Array of authentication types and corresponding authentication class names.
+    // Value is class name in SynchWeb\Authentication\Type namespace.
+    // Key is lower case representation of class name.
+    private $authentication_types = array(
+        'cas' => 'CAS',
+        'dummy' => 'Dummy',
+        'ldap' => 'LDAP',
+        'simple' => 'Simple',
+        'oidc' => 'OIDC',
+        'combined' => 'Combined',
+    );
+
+    // Return instance of authentication class corresponding to $authentication_type.
+    // The value passed by the calling method derives from $authentication_type, a global variable specified in config.php.
+    public function create($authentication_type)
+    {
+        if (!$authentication_type)
+        {
+            error_log("Authentication method not specified in config.php.");
+
+            $authentication_type = 'cas';
+        }
+
+        // Determine fully-qualified class name of authentication class corresponding to $authentication_type.
+        $full_class_name = null;
+
+        if (key_exists(strtolower($authentication_type), $this->authentication_types))
+        {
+            $full_class_name = 'SynchWeb\\Authentication\\Type\\' . $this->authentication_types[$authentication_type];
+        }
+        else
+        {
+            throw new \Exception("Authentication method '$authentication_type' not configured.");
+        }
+
+        // Return instance of authentication class.
+        if (class_exists($full_class_name))
+        {
+            return new $full_class_name();
+        }
+        else
+        {
+            throw new \Exception("Authentication class '$full_class_name' does not exist.");
+        }
+
+        throw new \Exception('Authentication not possible due to a configuration error.');
+    }
+}

api/src/Authentication/Type/CAS.php

@@ -8,6 +8,16 @@
 
 class CAS extends AuthenticationParent implements AuthenticationInterface
 {
+    function authorise()
+    {
+        return false;
+    }
+
+    function authenticateByCode($code)
+    {
+        return false;
+    }
+
     function check()
     {
         global $cas_url, $cas_sso, $cacert;

api/src/Authentication/Type/Combined.php

@@ -0,0 +1,39 @@
+<?php
+
+namespace SynchWeb\Authentication\Type;
+
+use SynchWeb\Authentication\AuthenticationInterface;
+use SynchWeb\Authentication\AuthenticationParent;
+
+/**
+ * Combined OIDC and CAS login to allow current api users to use the authentiate api
+ *  endpoint with username and password
+ */
+class Combined extends AuthenticationParent implements AuthenticationInterface
+{
+    private $CASAuth;
+    private $OIDCAuth;
+
+    function __construct() {
+        $this->CASAuth = new CAS();
+        $this->OIDCAuth = new OIDC();
+    }
+
+
+    public function authenticate($login, $password)
+    {
+        return $this->CASAuth->authenticate($login, $password);
+    }
+
+    public function check() {
+        return $this->OIDCAuth->check();
+    }
+
+    public function authorise() {
+        return $this->OIDCAuth->authorise();
+    }
+
+    public function authenticateByCode($code){
+        return $this->OIDCAuth->authenticateByCode($code);
+    }
+}

api/src/Authentication/Type/Dummy.php

@@ -7,6 +7,16 @@
 
 class Dummy extends AuthenticationParent implements AuthenticationInterface
 {
+    function authorise()
+    {
+        return false;
+    }
+
+    function authenticateByCode($code)
+    {
+        return false;
+    }
+
     function check()
     {
         return false;

api/src/Authentication/Type/LDAP.php

@@ -7,6 +7,16 @@
 
 class LDAP extends AuthenticationParent implements AuthenticationInterface
 {
+    function authorise()
+    {
+        return false;
+    }
+
+    function authenticateByCode($code)
+    {
+        return false;
+    }
+
     function check()
     {
         return false;