Merge pre-release/2024-R5.4 with master (#892)

* LIMS-1569: Get image viewer rings from dials if possible (#875)

* LIMS-1002: Fix error when creating new laboratory (#815)

* LIMS-1302 - add visit to container even if UAS fails (#762)

* LIMS-1487: Fix alphafold triggering (#866)

* LIMS-1563 - Remove touchscreen app (#867)

Co-authored-by: Mark Williams <mark.williams@diamond.ac.uk>
Co-authored-by: Guilherme Francisco <guilherme.de-freitas@diamond.ac.uk>

Author: 3 people

api/config_sample.php

@@ -128,12 +128,12 @@
     $enabled_container_types = array();
 
     # Zocalo message broker credentials - Set to empty string to disable
-    $zocalo_server = 'tcp://activemq.server.ac.uk';
-    $zocalo_username = 'foo';
-    $zocalo_password = 'bar';
-
-    # Primary Zocalo entry point for recipe submission
-    $zocalo_mx_reprocess_queue = '/queue/zocolo.name';
+    $rabbitmq_zocalo_host = 'rabbitmq.server.ac.uk';
+    $rabbitmq_zocalo_port = 5672;
+    $rabbitmq_zocalo_username = 'foo';
+    $rabbitmq_zocalo_password = 'bar';
+    $rabbitmq_zocalo_vhost = 'zocalo';
+    $rabbitmq_zocalo_routing_key = 'processing_recipe';
 
     # This is used to trigger Zocalo recipes on adding new Protein sequences
     # Set to empty string to disable
@@ -193,18 +193,6 @@
     $in_contacts = array('Ind Contact' => 'in@server.ac.uk'
                         );
 
-
-    # Beamline Sample Registration Machines
-    # - Used for touchscreen application (unauthenticated)
-    $blsr = array('1.2.3.4', # my touchscreen computer
-                  );
-
-    # Beamline Sample Registration IP -> Beamline mapping
-    # - Third part of ip is used to identify beamline
-    #   x.x.103.x => i03
-    $ip2bl = array(103 => 'i03',
-                   );
-
     # Barcode readers
     # - These clients use the android app (unauthenticated)
     $bcr = array('1.2.3.4', # my android device
@@ -393,4 +381,5 @@
     # Dials server values
     $dials_rest_url = "";
     $dials_rest_jwt = "";
+    $dials_rest_url_rings = false;
 ?>

api/index.php

@@ -71,7 +71,8 @@ function setupApplication($mode): Slim
             $facility_courier_countries, $facility_courier_countries_nde, $facility_courier_countries_link,
             $dhl_enable, $scale_grid, $scale_grid_end_date, $preset_proposal, $timezone,
             $valid_components, $enabled_container_types, $ifsummary, $synchweb_version, $redirects,
-            $shipping_service_app_url, $use_shipping_service_redirect, $use_shipping_service_redirect_incoming_shipments;
+            $shipping_service_app_url, $use_shipping_service_redirect, $use_shipping_service_redirect_incoming_shipments,
+            $dials_rest_url_rings;
         $app->contentType('application/json');
         $options = $app->container['options'];
         $app->response()->body(json_encode(array(
@@ -95,6 +96,7 @@ function setupApplication($mode): Slim
             'synchweb_version' => $synchweb_version,
             'shipping_service_app_url' => $use_shipping_service_redirect || $use_shipping_service_redirect_incoming_shipments ? $shipping_service_app_url : null,
             'shipping_service_app_url_incoming' => $use_shipping_service_redirect_incoming_shipments ? $shipping_service_app_url : null,
+            'dials_rest_url_rings' => $dials_rest_url_rings,
             'redirects' => $redirects
         )));
     });

api/src/Controllers/AssignController.php

@@ -13,7 +13,7 @@ class AssignController extends Page
 
     public static $arg_list = array('visit' => '\w+\d+-\d+', 'cid' => '\d+', 'did' => '\d+', 'pos' => '\d+', 'bl' => '[\w\-]+');
 
-    public static $dispatch = array(array('/visits(/:visit)', 'get', 'getBeamlineVisits'),
+    public static $dispatch = array(
             array('/assign', 'get', 'assignContainer'),
             array('/unassign', 'get', 'unassignContainer'),
             array('/deact', 'get', 'deactivateDewar'),
@@ -74,30 +74,6 @@ function deactivateDewar()
         }
     }
 
-
-    # ------------------------------------------------------------------------
-    # Return visits for beamline
-    function getBeamlineVisits($visit = null)
-    {
-        $visits = $this->blsr_visits();
-
-        if ($visit)
-        {
-            foreach ($visits as $i => $v)
-            {
-                if ($v['VISIT'] == $visit)
-                {
-                    $this->_output($v);
-                    return;
-                }
-            }
-            $this->_error('No such visit');
-        }
-        else
-            $this->_output($visits);
-    }
-
-
     # ------------------------------------------------------------------------
     # Puck names from puck scanner
     # BL03I-MO-ROBOT-01:PUCK_01_NAME

api/src/Controllers/AuthenticationController.php

@@ -89,7 +89,7 @@ function check()
 
     private function checkAuthRequiredForSpecificSituations($parts): bool
     {
-        global $blsr, $bcr, $img, $auto;
+        global $bcr, $img, $auto;
 
         $need_auth = true;
         # Work around to allow beamline sample registration without CAS authentication
@@ -102,10 +102,6 @@ private function checkAuthRequiredForSpecificSituations($parts): bool
                 # Allow formulatrix machines unauthorised access to inspections, certain IPs only
             ($parts[0] == 'imaging' && $parts[1] == 'inspection' && in_array($_SERVER["REMOTE_ADDR"], $img)) ||
 
-                # For use on the touchscreen computers in the hutch.
-                # Handles api calls: /assign/visits/<vist> e.g./assign/visits/mx1234-1
-            ($parts[0] == 'assign' && $parts[1] == 'visits' && in_array($_SERVER["REMOTE_ADDR"], $blsr)) ||
-
                 # Allow barcode reader ips unauthorised access to add history
             ($parts[0] == 'shipment' && $parts[1] == 'dewars' && $parts[2] == 'history' && in_array($_SERVER["REMOTE_ADDR"], $bcr)) ||
 
@@ -129,11 +125,6 @@ private function checkAuthRequiredForSpecificSituations($parts): bool
         else if (sizeof($parts) >= 2)
         {
             if (
-                # For use on the touchscreen computers in the hutch
-                # Handles api calls: /assign/assign, /assign/unassign, /assign/deact, /assign/visits
-            (($parts[0] == 'assign') && in_array($_SERVER["REMOTE_ADDR"], $blsr)) ||
-            (($parts[0] == 'shipment' && $parts[1] == 'containers') && in_array($_SERVER["REMOTE_ADDR"], $blsr)) ||
-
                 # Allow barcode reader unauthorised access, same as above, certain IPs only
             ($parts[0] == 'shipment' && $parts[1] == 'dewars' && in_array($_SERVER["REMOTE_ADDR"], $bcr)) ||
 

api/src/Controllers/UserController.php

@@ -275,13 +275,8 @@ function _update_user()
         $person = $this->userData->getUser($this->user->personId, $this->proposalid, $this->arg('PERSONID'));
         $person = $person[0];
         $this->_output((array) $person);
-        $laboratory = null;
-        if ($person['LABORATORYID'])
-        {
-            $laboratory = $this->userData->getLaboratory($person['LABORATORYID'])[0];
-        }
 
-        $this->userData->updateLaboratory(
+        $laboratoryId = $this->userData->updateLaboratory(
             $this->arg('PERSONID'),
             $this->argOrNull('LABNAME'),
             $this->argOrNull('ADDRESS'),
@@ -290,7 +285,7 @@ function _update_user()
             $this->argOrNull('COUNTRY'),
             $person['LABORATORYID']
         );
-        $laboratory = $this->userData->getLaboratory($person['LABORATORYID']);
+        $laboratory = $this->userData->getLaboratory($laboratoryId);
         $this->_output((array) $laboratory[0]);
     }
 
@@ -362,4 +357,4 @@ function _update_permission()
         );
         $this->_output(array('TYPE' => $this->arg('TYPE'), 'DESCRIPTION' => $desc));
     }
-}
+}

api/src/Model/Services/UserData.php

@@ -340,6 +340,7 @@ function updateLaboratory($personId, $labName, $labAddress, $city, $postcode, $c
                 ->whereIdEquals("personid", $personId)
                 ->update("person");
         }
+        return $laboratoryId;
     }
 
     function addGroupUser($personId, $gid)

api/src/Page.php

@@ -222,29 +222,8 @@ function auth($require_staff)
         {
             $auth = $this->staff;
 
-            // Beamline Sample Registration
-        }
-        else if ($this->blsr() && !$this->user->loginId)
-        {
-            $auth = false;
-
-            if ($this->has_arg('visit'))
-            {
-                $blsr_visits = array();
-                foreach ($this->blsr_visits() as $v)
-                    array_push($blsr_visits, $v['VISIT']);
-
-                if (in_array($this->arg('visit'), $blsr_visits))
-                    $auth = True;
-
-            }
-            else
-            {
-                $auth = true;
-            }
-
-            // Barcode Scanners
         }
+        // Barcode Scanners
         else if ($this->bcr() && !$this->user->loginId)
         {
             $auth = true;
@@ -761,42 +740,6 @@ function pro()
     }
 
 
-    # ------------------------------------------------------------------------
-    # Beamline sample registration: Get Beamline from IP
-    function ip2bl()
-    {
-        global $ip2bl;
-        $parts = explode('.', $_SERVER['REMOTE_ADDR']);
-
-        if ($parts && sizeof($parts) > 1 && array_key_exists($parts[2], $ip2bl))
-        {
-            return $ip2bl[$parts[2]];
-        }
-    }
-
-
-    # Return visit list for blsr;
-    function blsr_visits()
-    {
-        $b = $this->ip2bl();
-
-        if (!$b)
-            return array();
-
-        $visits = $this->db->pq("SELECT CONCAT(p.proposalcode, p.proposalnumber, '-', s.visit_number) as visit, TO_CHAR(s.startdate, 'DD-MM-YYYY HH24:MI') as st, TO_CHAR(s.enddate, 'DD-MM-YYYY HH24:MI') as en,s.beamlinename as bl FROM blsession s INNER JOIN proposal p ON (p.proposalid = s.proposalid) WHERE TIMESTAMPDIFF('DAY', s.startdate, CURRENT_TIMESTAMP) < 1 AND TIMESTAMPDIFF('DAY', CURRENT_TIMESTAMP, s.enddate) < 2 AND s.beamlinename LIKE :1 ORDER BY s.startdate", array($b));
-        $v = $this->db->paginate("SELECT CONCAT(p.proposalcode, p.proposalnumber, '-', s.visit_number) as visit, TO_CHAR(s.startdate, 'DD-MM-YYYY HH24:MI') as st, TO_CHAR(s.enddate, 'DD-MM-YYYY HH24:MI') as en,s.beamlinename as bl FROM blsession s INNER JOIN proposal p ON (p.proposalid = s.proposalid) WHERE p.proposalcode LIKE 'cm' AND s.beamlinename LIKE :1 AND s.enddate <= CURRENT_TIMESTAMP ORDER BY s.startdate DESC", array($b, 0, 1));
-        $visits = array_merge($visits, $v);
-        return $visits;
-    }
-
-    # Beamline Sample Registration Machine
-    function blsr()
-    {
-        global $blsr;
-
-        return in_array($_SERVER['REMOTE_ADDR'], $blsr);
-    }
-
     # Barcode Scanner Machines
     function bcr()
     {
@@ -1093,9 +1036,9 @@ function get_visit_processed_dir($dc, $location)
 
     function _submit_zocalo_recipe($recipe, $parameters, $error_code = 500)
     {
-        global $zocalo_mx_reprocess_queue;
+        global $rabbitmq_zocalo_vhost;
 
-        if (isset($zocalo_mx_reprocess_queue))
+        if (isset($rabbitmq_zocalo_vhost))
         {
             // Send job to processing queue
             $zocalo_message = array(
@@ -1104,7 +1047,7 @@ function _submit_zocalo_recipe($recipe, $parameters, $error_code = 500)
                 ),
                 'parameters' => $parameters,
             );
-            $this->_send_zocalo_message($zocalo_mx_reprocess_queue, $zocalo_message, $error_code);
+            $this->_send_zocalo_message($rabbitmq_zocalo_vhost, $zocalo_message, $error_code);
         }
     }
 
@@ -1130,7 +1073,6 @@ function _send_zocalo_message($rabbitmq_zocalo_vhost, $zocalo_message, $error_co
 
         try
         {
-            error_log("Sending message" . var_export($zocalo_message, true));
             $queue = new Queue($rabbitmq_zocalo_host, $rabbitmq_zocalo_port, $rabbitmq_zocalo_username, $rabbitmq_zocalo_password, $rabbitmq_zocalo_vhost);
             $queue->send($zocalo_message, $rabbitmq_zocalo_routing_key);
         }

api/src/Page/Image.php

@@ -20,11 +20,13 @@ class Image extends Page
             'aid' => '\d+', 
             'visit' => '\w+\d+-\d+',
             'thresh' => '\d',
+            'res' => '\d',
+            'ice' => '\d',
         );
 
         public static $dispatch = array(array('/id/:id(/n/:n)', 'get', '_xtal_image'),
                               array('/diff/id/:id(/f/:f)(/n/:n)', 'get', '_diffraction_image'),
-                              array('/di/id/:id(/thresh/:thresh)(/n/:n)', 'get', '_diffraction_viewer'),
+                              array('/di/id/:id(/thresh/:thresh)(/res/:res)(/ice/:ice)(/n/:n)', 'get', '_diffraction_viewer'),
                               array('/cam/bl/:bl(/n/:n)', 'get', '_forward_webcam'),
                               array('/oav/bl/:bl(/n/:n)', 'get', '_forward_oav'),
                               array('/fa/fid/:id', 'get', '_fault_attachment'),
@@ -192,7 +194,7 @@ function _diffraction_viewer() {
             }
 
             $im = $info['LOC'] . '/' . $info['FT'];
-            $out = '/tmp/' . $this->arg('id') . '_' . $n . ($this->has_arg('thresh') ? '_th' : '') . '.jpg';
+            $out = '/tmp/' . $this->arg('id') . '_' . $n . ($this->has_arg('thresh') ? '_th' : '') . ($this->has_arg('res') ? '_res' : '') . ($this->has_arg('ice') ? '_ice' : '') . '.jpg';
             global $dials_rest_url, $dials_rest_jwt;
             if (!file_exists($out)) {                
                 if (!empty($dials_rest_url) && !empty($dials_rest_jwt)) {
@@ -212,6 +214,8 @@ function _diffraction_viewer() {
                             'colour_scheme' => 'greyscale',
                             'brightness' => $this->has_arg('thresh') ? 1000 : 10,
                             'format' => 'png',
+                            'resolution_rings' => array('show' => $this->has_arg('res')),
+                            'ice_rings' => array('show' => $this->has_arg('ice')),
                         )
                     ));
                 } else {

api/src/Page/Proposal.php

@@ -1205,8 +1205,8 @@ function _update_autocollect_session($sessionId, $uasSessionId, $containerId, $t
             $uas = new UAS($auto_user, $auto_pass);
             $code = $uas->update_session($uasSessionId, $data);
 
-            if ($code == 200) {
-                // Update ISPyB records
+            if ($code == 200 || $code == 404) {
+                // Update ISPyB records, even if UAS says session not found
                 $this->db->pq("UPDATE container SET sessionid=:1 WHERE containerid=:2", array($sessionId, $containerId));
                 // For debugging - actually just want to return Success!
                 $result = array(
@@ -1216,13 +1216,11 @@ function _update_autocollect_session($sessionId, $uasSessionId, $containerId, $t
                 );
             } else if ($code == 403) {
                 $this->_error('UAS Error - samples and/or investigators not valid. ISPyB/UAS Session ID: ' . $sessionId . ' / ' . $uasSessionId);
-            } else if ($code == 404) {
-                $this->_error('UAS Error - session not found in UAS, Session ID: ' . $sessionId . ' UAS Session ID: ' . $uasSessionId);
             } else {
-                $this->_error('UAS Error - something wrong creating a session for that container ' . $containerId . ', response code was: ' . $code);
+                $this->_error('UAS Error - something went wrong updating a session for that container ' . $containerId . ', response code was: ' . $code);
             }
         } else {
-            error_log("Something wrong - an Auto Collect session exists but with no containers " . $sessionId);
+            error_log("Something went wrong - an Auto Collect session exists but with no containers " . $sessionId);
 
             $this->_error('No valid containers on the existing Auto Collect Session id:', $sessionId);
         }