Merge pull request #687 from DiamondLightSource/pre-release/2023-R4.3

Pre release/2023 r4.3
DiamondLightSource · Nov 2, 2023 · aa9dfcd · aa9dfcd
2 parents 7d6f57f + f03a8d5
commit aa9dfcd
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Showing 10 changed files with 100 additions and 45 deletions.
diff --git a/api/config_sample.php b/api/config_sample.php
@@ -43,7 +43,7 @@
     # CAS CA Cert (for SSO)
     $cacert = '/etc/certs/ca-bundle.crt';
 
-    # ldap server, used for lookup and authentication (if using)
+    # ldap server, used for lookup and authentication (if using, set to null if not)
     # Update the ldap(s) prefix, hostname and search settings as required
     $ldap_server = 'ldaps://ldap.example.com';
     $ldap_search = 'ou=people,dc=example,dc=com';
@@ -248,7 +248,10 @@
     # Shipping service details
     $use_shipping_service = null;
     $use_shipping_service_incoming_shipments = null;
-    $shipping_service_url = null;
+    $shipping_service_api_url = null;
+    $shipping_service_api_user = null;
+    $shipping_service_api_password = null;
+    $shipping_service_app_url = null;
     $shipping_service_links_in_emails = null;
 
 

diff --git a/api/index.php b/api/index.php
@@ -24,6 +24,7 @@
 use SynchWeb\Database\DatabaseParent;
 use SynchWeb\ImagingShared;
 use SynchWeb\Dispatch;
+use SynchWeb\Options;
 
 require 'vendor/autoload.php';
 
@@ -71,8 +72,9 @@ function setupApplication($mode): Slim
             $dhl_enable, $dhl_link, $scale_grid, $scale_grid_end_date, $preset_proposal, $timezone,
             $valid_components, $enabled_container_types, $ifsummary;
         $app->contentType('application/json');
+        $options = $app->container['options'];
         $app->response()->body(json_encode(array(
-            'motd' => $motd,
+            'motd' => $options->get('motd', $motd),
             'authentication_type' => $authentication_type,
             'cas_url' => $cas_url,
             'cas_sso' => $cas_sso,
@@ -145,4 +147,8 @@ function setupDependencyInjectionContainer($app)
     $app->container->singleton('dispatch', function () use ($app) {
         return new Dispatch($app, $app->container['db'], $app->container['user']);
     });
+
+    $app->container->singleton('options', function () use ($app) {
+        return new Options($app->container['db']);
+    });
 }
diff --git a/api/src/Authentication/Type/OIDC.php b/api/src/Authentication/Type/OIDC.php
@@ -18,14 +18,22 @@ function __construct() {
         curl_setopt($ch, CURLOPT_HEADER, 0);
         curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
         $response = curl_exec($ch);
+        $http_code = curl_getinfo($ch, CURLINFO_HTTP_CODE);
+        $errno = curl_errno($ch);
+
+        if ($errno || $http_code != 200) {
+            error_log("Failed to connect to OIDC discovery endpoint. HTTP code: " . $http_code . ". CURL err. no.: " . $errno);
+            return;
+        }
+
         curl_close($ch);
         $newProviderConfig = json_decode($response);
 
         if(!$newProviderConfig
             || !isset($newProviderConfig->userinfo_endpoint)
             || !isset($newProviderConfig->authorization_endpoint) 
             || !isset($newProviderConfig->token_endpoint)) {
-            error_log("OIDC Authentication provider replied with invalid JSON body");
+            error_log("OIDC Authentication provider replied with invalid JSON discovery body");
             return;
         }
         $newProviderConfig->b64ClientCreds = base64_encode(

diff --git a/api/src/Options.php b/api/src/Options.php
@@ -21,7 +21,7 @@ private function _retrieve() {
 
             $this->options = array();
             foreach ($options as $o) {
-                $this->options[$o['NAME']] = unserialize($o['VALUE']);
+                $this->options[$o['NAME']] = $o['VALUE'];
                 if ($o['UI'] == 1) $this->public[$o['NAME']] = $this->options[$o['NAME']];
 
             }

diff --git a/api/src/Page.php b/api/src/Page.php
@@ -915,6 +915,10 @@ function _ldap_search($search, $email = False)
         global $ldap_server, $ldap_search;
 
         $ret = array();
+        if (is_null($ldap_server)) {
+            error_log("Ldap server is not configured, not looking up user.");
+            return $ret;
+        }
         $ds = ldap_connect($ldap_server);
         if ($ds)
         {

diff --git a/api/src/Page/Contact.php b/api/src/Page/Contact.php
@@ -167,7 +167,7 @@ function _add_contact() {
                     foreach ($lfields as $i => $f) {
                         if ($this->has_arg($f)) {
                             $c = $f == 'LABNAME' ? 'NAME' : $f;
-                            $this->db->pq('UPDATE laboratory SET '.$c.'=:1 WHERE laboratoryid=:2', array($this->arg($f), $lab['LABORATORYID']));
+                            $this->db->pq('UPDATE laboratory SET '.$c.'=:1 WHERE laboratoryid=:2', array($this->arg($f), $lab[0]['LABORATORYID']));
                         }
                     }
                 }

diff --git a/api/src/Page/Shipment.php b/api/src/Page/Shipment.php
@@ -927,10 +927,10 @@ function _dispatch_dewar_in_shipping_service($dispatch_info, $dewar)
         global $facility_country;
         global $facility_phone;
         global $facility_contact;
-        global $shipping_service_url;
+        global $shipping_service_api_url;
         global $facility_email;
-        if (!isset($shipping_service_url)) {
-            throw new Exception("Could not send request to shipping service: shipping_service_url not set");
+        if (!isset($shipping_service_api_url)) {
+            throw new Exception("Could not send request to shipping service: shipping_service_api_url not set");
         }
 
         # Create shipment
@@ -2613,46 +2613,57 @@ function _add_shipment()
 
     function _get_default_dewar()
     {
-        if (!$this->has_arg('visit'))
-            $this->_error('No visit specified');
-
-        $sids = $this->db->pq("SELECT s.sessionid FROM blsession s INNER JOIN proposal p ON p.proposalid = s.proposalid WHERE CONCAT(p.proposalcode, p.proposalnumber, '-', s.visit_number) LIKE :1 AND p.proposalid=:2", array($this->arg('visit'), $this->proposalid));
-
-        if (!sizeof($sids))
-            $this->_error('No such visit');
-        else
-            $sid = $sids[0]['SESSIONID'];
+        if ($this->has_arg('visit')) {
+            $shipmentName = $this->arg('visit') . '_Shipment1';
+            $dewarName = $this->arg('visit') . '_Dewar1';
+            $sids = $this->db->pq("SELECT s.sessionid FROM blsession s INNER JOIN proposal p ON p.proposalid = s.proposalid WHERE CONCAT(p.proposalcode, p.proposalnumber, '-', s.visit_number) LIKE :1 AND p.proposalid=:2", array($this->arg('visit'), $this->proposalid));
+            if (!sizeof($sids))
+                $this->_error('No such visit');
+            else
+                $sid = $sids[0]['SESSIONID'];
 
+        } elseif ($this->has_arg('prop')) {
+            $shipmentName = $this->arg('prop') . '_Shipment1';
+            $dewarName = $this->arg('prop') . '_Dewar1';
+            $sid = null;
+        } else {
+            $this->_error('No visit or proposal specified');
+        }
 
-        $shids = $this->db->pq("SELECT shippingid FROM shipping WHERE proposalid LIKE :1 AND shippingname LIKE :2", array($this->proposalid, $this->arg('visit') . '_Shipment1'));
+        $shids = $this->db->pq("SELECT shippingid FROM shipping WHERE proposalid LIKE :1 AND shippingname LIKE :2", array($this->proposalid, $shipmentName));
 
         if (sizeof($shids) > 0) {
             $shid = $shids[0]['SHIPPINGID'];
         } else {
-            $this->db->pq("INSERT INTO shipping (shippingid,proposalid,shippingname,bltimestamp,creationdate,shippingstatus) VALUES (s_shipping.nextval,:1,:2,CURRENT_TIMESTAMP,CURRENT_TIMESTAMP,'processing') RETURNING shippingid INTO :id", array($this->proposalid, $this->arg('visit') . '_Shipment1'));
+            $this->db->pq("INSERT INTO shipping (shippingid,proposalid,shippingname,bltimestamp,creationdate,shippingstatus) VALUES (s_shipping.nextval,:1,:2,CURRENT_TIMESTAMP,CURRENT_TIMESTAMP,'processing') RETURNING shippingid INTO :id", array($this->proposalid, $shipmentName));
 
             $shid = $this->db->id();
-
-            $vals = $this->db->pq("INSERT INTO shippinghassession (shippingid,sessionid) VALUES (:1,:2)", array($shid, $sid));
+            if ($sid)
+                $vals = $this->db->pq("INSERT INTO shippinghassession (shippingid,sessionid) VALUES (:1,:2)", array($shid, $sid));
         }
 
         $did = -1;
-        if ($sid) {
-            $dids = $this->db->pq("SELECT dewarid from dewar WHERE shippingid LIKE :1 AND code LIKE :2", array($shid, $this->arg('visit') . '_Dewar1'));
 
-            if (sizeof($dids) > 0) {
-                $did = $dids[0]['DEWARID'];
-            } else {
-                $this->db->pq("INSERT INTO dewar (dewarid,code,shippingid,bltimestamp,dewarstatus,firstexperimentid) VALUES (s_dewar.nextval,:1,:2,CURRENT_TIMESTAMP,'processing',:3) RETURNING dewarid INTO :id", array($this->arg('visit') . '_Dewar1', $shid, $sid));
+        $dids = $this->db->pq("SELECT dewarid from dewar WHERE shippingid LIKE :1 AND code LIKE :2", array($shid, $dewarName));
+
+        if (sizeof($dids) > 0) {
+            $did = $dids[0]['DEWARID'];
+        } else {
+            $this->db->pq("INSERT INTO dewar (dewarid,code,shippingid,bltimestamp,dewarstatus,firstexperimentid) VALUES (s_dewar.nextval,:1,:2,CURRENT_TIMESTAMP,'processing',:3) RETURNING dewarid INTO :id", array($dewarName, $shid, $sid));
 
-                $did = $this->db->id();
+            $did = $this->db->id();
 
-                # Need to generate barcode
+            # Need to generate barcode
+            if ($this->has_arg('visit')) {
                 $bl = $this->db->pq("SELECT s.beamlinename as bl FROM blsession s WHERE s.sessionid=:1", array($sid));
-                $this->db->pq("UPDATE dewar set barcode=:1 WHERE dewarid=:2", array($this->arg('visit') . '-' . $bl[0]['BL'] . '-' . str_pad($did, 7, '0', STR_PAD_LEFT), $did));
+                $barcode = $this->arg('visit') . '-' . $bl[0]['BL'] . '-' . str_pad($did, 7, '0', STR_PAD_LEFT);
+            } else {
+                $barcode = $this->arg('prop') . '-' . str_pad($did, 7, '0', STR_PAD_LEFT);
             }
+            $this->db->pq("UPDATE dewar set barcode=:1 WHERE dewarid=:2", array($barcode, $did));
         }
 
+
         if ($did == -1)
             $this->_error('Couldn\'t create default dewar');
         $this->_output($did);

diff --git a/api/src/Shipment/ShippingService.php b/api/src/Shipment/ShippingService.php
@@ -9,29 +9,53 @@
 class ShippingService
 {
     private $shipping_api_url;
-    private $headers;
+    private $shipping_app_url;
     public const JOURNEY_TO_FACILITY = "TO_FACILITY";
     public const JOURNEY_FROM_FACILITY = "FROM_FACILITY";
 
-    function __construct()
+    function _build_headers()
     {
-        global $shipping_service_url;
-        $this->shipping_api_url = $shipping_service_url;
-        $this->headers = array(
+        global $cookie_key;
+        global $shipping_service_api_user;
+        global $shipping_service_api_password;
+
+        $headers = array(
             'Accept: application/json',
             'Content-Type: application/json',
         );
+
+        if (isset($_COOKIE[$cookie_key])) {
+            array_push($headers, "Authorization: Bearer {$_COOKIE[$cookie_key]}");
+            return $headers;
+        }
+
+        if (isset($shipping_service_api_user) && isset($shipping_service_api_password)) {
+            $basic_auth = base64_encode($shipping_service_api_user . ":" . $shipping_service_api_password);
+            array_push($headers, "Authorization: Basic {$basic_auth}");
+            return $headers;
+        }
+
+        throw new \Exception("Shipping service auth error: no cookie found and basic auth credentials unset");
+    }
+
+    function __construct()
+    {
+        global $shipping_service_api_url;
+        global $shipping_service_app_url;
+        $this->shipping_api_url = $shipping_service_api_url;
+        $this->shipping_app_url = $shipping_service_app_url;
     }
 
 
     function _send_request($url, $type, $data, $expected_status_code)
     {
         $ch = curl_init($url);
+        $base_headers = $this->_build_headers();
         curl_setopt_array(
             $ch,
             array(
                 CURLOPT_RETURNTRANSFER => TRUE,
-                CURLOPT_HTTPHEADER => $this->headers,
+                CURLOPT_HTTPHEADER => $base_headers,
                 CURLOPT_TIMEOUT => 5
             )
         );
@@ -52,7 +76,7 @@ function _send_request($url, $type, $data, $expected_status_code)
                     $ch,
                     array(
                         CURLOPT_CUSTOMREQUEST => "PUT",
-                        CURLOPT_HTTPHEADER => array_merge($this->headers, array('Content-Length: ' . strlen(json_encode($data)))),
+                        CURLOPT_HTTPHEADER => array_merge($base_headers, array('Content-Length: ' . strlen(json_encode($data)))),
                         CURLOPT_POSTFIELDS => json_encode($data),
                     )
                 );
@@ -125,6 +149,6 @@ function dispatch_shipment($shipment_id, $pickup_requested)
 
     function get_awb_pdf_url($shipment_id)
     {
-        return $this->shipping_api_url . '/shipments/' . $shipment_id . '/awb/pdf';
+        return $this->shipping_app_url . '/shipments/' . $shipment_id . '/awb';
     }
 }
diff --git a/client/src/js/modules/fault/routes.js b/client/src/js/modules/fault/routes.js
@@ -85,6 +85,7 @@ const routes = [
             {
                 path: 'edit',
                 name: 'faults-view-edit',
+                component: MarionetteView,
                 props: {
                     mview: FaultTypeEditor,
                     breadcrumbs: [bc, { title: 'Edit Fault Types' }],
@@ -102,4 +103,4 @@ const routes = [
     },
 ]
 
-export default routes
+export default routes
diff --git a/client/src/js/modules/types/xpdf/samples/views/vue-simplesample.vue b/client/src/js/modules/types/xpdf/samples/views/vue-simplesample.vue
@@ -406,10 +406,8 @@
         methods: {
             async setDewarInformation() {
               // Try to retrieve the default dewar for this proposal/visit
-              // Uses the special session-0 because at this point we are not necessarily on a session
               this.defaultDewarId = await this.$store.dispatch('fetchDataFromApi', {
                 url: '/shipment/dewars/default',
-                data: { visit: `${this.$store.getters['proposal/currentProposal']}-0`},
                 requestType: 'fetching default dewar for this proposal/visit'
               })
             },
@@ -542,7 +540,7 @@
                     })
 
                     let container = new Container({
-                        NAME: app.prop + '-' + app.visit + '_samples',
+                        NAME: app.visit ? app.prop + '-' + app.visit + '_samples' : app.prop + '_samples',
                         CAPACITY: self.capacity,
                         CONTAINERTYPE: 'Box',
                         COMMENTS: item.comments
@@ -620,7 +618,7 @@
                 })
 
                 let container = new Container({
-                    NAME: app.prop + '-' + app.visit + '_samples',
+                    NAME: app.visit ? app.prop + '-' + app.visit + '_samples' : app.prop + '_samples',
                     CAPACITY: this.capacity,
                     CONTAINERTYPE: 'Box',
                     COMMENTS: this.comments
@@ -840,4 +838,4 @@
             }
         }
     }
-</script>
+</script>